Citrus Sinensis ID: 003463

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------82
Protein Sequence
MNWDCKVSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVNFQVCPSNGSHLRDASGSPIADDEGNKPENS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEcccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcHHHHHcccccccEEEEEccccHHHHHHHHHHHHHcccccccEEEEccccccccccEEEEEEccccccHHHHHHHHccccccccccccEEEEEEHHHHcHHHHHHHHccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccHHHHcHHHHcccccccHHHHHHHHHccccccccccccccHHHccccccccccEEEccccccHHHHccEEEcccccccccHHHcccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEcccccccEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcHHHHHccccccEEEEEEcccccHHHHHHHHHHHHHccccEEEEEEEEcccccccEEEEEEEcccHHHHHHHHHHHcccccEEccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mnwdckvsslpvlpheklnlnamglgrqsvddissglskvhhgvasddplegvmnpaignslpddeDELLAGimddfdlrglpssledledydifgsgggmelegepqeslsmsmskisisdsasgngllhysvpngagtvagehpygehpsrtLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQnkplrrrkldihfsipkdnpsdkdlnqgtlvvfnldpsvsnedLRQIFGAYGevkeiretphkrhhkFIEFYDVRAAEAALKSLnrsdiagkriklepsrpggarRNLMLQLNQELEQDESRILqhqvgspitnsppgnwvqfsspiehnplqtiskspnfrnmspttsnhmpglasilhpqvstlekiapigkdqgrgslMEHALTntisangasfqqsnsfsepkiglyrgtvssfgpspsngsgvetlsgpqflwgspsrysehssspawqtssmghpfssngkihglpysgrqgsflgssqhhhvgsapsgvplerrfgflpespetsfmnpvafcgmgigqndgsfmvnmgsrasvnpgitvprnlsdngssfrvmssprlspvflgngpypgltpanieGLYERGrsrriennngnqldsKKQFQLELEKIrsgedtrtTLMIKNIPNKYTSKMLLAAIDEnhkgtydflylpidfknkcnVGYAFINmlsplhiipfyeafngkkwekfNSEKVASLAYARIQGRAALVAHFqnsslmnedkrcrpilfhsegpeagdqvtqeqlnsnsvnfqvcpsngshlrdasgspiaddegnkpens
Flexible Loop (DISEMBL)
mnwdckvsslpvlpHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRalqnkplrrrKLDIhfsipkdnpsdkdlnQGTLVVFNldpsvsneDLRQIFGAYGEvkeiretphkrhhKFIEFYDVRAAEAALKslnrsdiagkriklepsrpggarrNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRriennngnqldskkqFQLELEkirsgedtrttlmiknipnkYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVNFQVCPSNgshlrdasgspiaddegnkpens
Low Complexity Region (SEG)
MNWDCKVSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEslsmsmskisisdsasGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMlqlnqeleqdeSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVssfgpspsngsgVETLSGPQFLWGspsrysehsssPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVNFQVCPSNGSHLRDASGSPIADDEGNKPENS
Disordered region (IsUnstruct)
********************************************************************LLAGIMDDFDLRGL********DYDIF**********************************LHYSV******************RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK*LR*RKLDIHF*************QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK**********************************************************************************************************************************************************************************************************************************************************FMNPVAFCGMGIGQNDGSFMVN**********************************VFLGNGPYPGLT***I****************************************TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSL******CRPILF****************************************************
Disordered Region (DISOPRED)
**********PVLPH*******************************************GNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQES***************************************H**RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI******************LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG***************************************************************************************************************************************************************************************************************************************************************************************************************************************FQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSE*************************************************
Disordered Region (DISEMBL)
********SLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMEL**********SMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGS*******************HPFSSNGKIHGLPYSGRQGSFLG************GVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVNFQVCPSNG**********************
Disordered Region (DISPRO)
*****KVSSLPVLPHEKLNLNAMG*****V**ISSGL******VASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGL*******************EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS***LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP*************************Q*GSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASI*HPQVSTLEKIA***KDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPS*SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERG***************KKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSE*************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNWDCKVSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVNFQVCPSNGSHLRDASGSPIADDEGNKPENS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	818	2.2.26 [Sep-21-2011]
Q6ZI17	848	Protein MEI2-like 2 OS=Or	yes	no	0.947	0.913	0.600	0.0
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	yes	no	0.902	0.922	0.628	0.0
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.858	0.924	0.574	0.0
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.885	0.892	0.520	0.0
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.938	0.911	0.479	0.0
Q75M35	955	Protein MEI2-like 3 OS=Or	no	no	0.849	0.727	0.414	1e-134
Q64M78	1001	Protein MEI2-like 4 OS=Or	no	no	0.371	0.303	0.529	6e-79
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.311	0.281	0.569	4e-72
Q8W4I9	915	Protein MEI2-like 1 OS=Ar	no	no	0.293	0.262	0.494	1e-58
P08965	750	Meiosis protein mei2 OS=S	yes	no	0.141	0.154	0.548	9e-37

>sp|Q6ZI17|OML2_ORYSJ Protein MEI2-like 2 OS=Oryza sativa subsp. japonica GN=ML2 PE=2 SV=1

 Score =  920 bits (2378), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 490/816 (60%), Positives = 587/816 (71%), Gaps = 41/816 (5%)

Query: 8   SSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDED 67
           +SLPVLPHEK+N      G   +DD S+ L ++       D         I + LP+ ED
Sbjct: 53  TSLPVLPHEKINFLDSARGTPLMDDASAKLKELDDDPEGKDYKFDFDLRQIDDLLPN-ED 111

Query: 68  ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN 127
           +L AGI ++ +  G  +S+E+LE++D+FGSGGGMEL+ +P ES++  +   SI+D   GN
Sbjct: 112 DLFAGITNEIEPAGQTNSMEELEEFDVFGSGGGMELDTDPVESITAGLGNTSIADGLRGN 171

Query: 128 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 187
           G+ H+   N A TVAGEHPYGEHPSRTLFVRNINSNV+D+ELR+LFEQYGDIRTLYTA K
Sbjct: 172 GVNHFGPSNSASTVAGEHPYGEHPSRTLFVRNINSNVDDTELRSLFEQYGDIRTLYTATK 231

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 247
           HRGFVMISY+DIRAAR AMR LQNKPLRRRKLDIHFSIPK+NPSDKDLNQGTLV+FNLDP
Sbjct: 232 HRGFVMISYFDIRAARGAMRGLQNKPLRRRKLDIHFSIPKENPSDKDLNQGTLVIFNLDP 291

Query: 248 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
           SVSNE++RQIFG YGEVKEIRETP+K+HHKFIEFYDVRAAEAAL+SLN+S+IAGKRIKLE
Sbjct: 292 SVSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALRSLNKSEIAGKRIKLE 351

Query: 308 PSRPGGARRNLMLQLNQELEQDESRILQ-HQVGSPITNSPPGNWVQFSSPIEHNPLQTIS 366
           PSRPGG RRNLM QL  +++QDE R  +   VGSPI +SPPG W Q+SSP ++N LQ  +
Sbjct: 352 PSRPGGTRRNLMQQLGHDIDQDEPRSYRIPHVGSPIASSPPGAWAQYSSPTDNNLLQAFN 411

Query: 367 KSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGAS 426
            SP    MSP       G+   L   +S   KIAPIGKD    S  +   +N    +GA+
Sbjct: 412 ASPTGNGMSPI------GMPPSL---ISNAVKIAPIGKDS-NWSKYDKVFSNNNQPHGAA 461

Query: 427 FQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTS 486
           FQ S+S+ + K             S    S   TL+GP+FLWGSP  YSEH+ SP W+  
Sbjct: 462 FQHSHSYQDHK-------------SEHMSSSPGTLTGPEFLWGSPKPYSEHAQSPIWRPP 508

Query: 487 SMGHPFSSNGKI--HGLPYSGRQGSFLGSS---QHHHVGSAPSGVPLERRFGFLPESPET 541
           ++GH   SN +    GL Y GRQ S  GS     HHHVGSAPSG P E  FGFLPESPET
Sbjct: 509 AIGHAIPSNTRSQGQGLLYGGRQASLFGSQDQLHHHHVGSAPSGAPFESHFGFLPESPET 568

Query: 542 SFMNPVAF---CGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSD-NGSSFRVMSSPRLS 597
           S+MN V F     +G G+N    M+NM +RASVNP   +  N+SD N SSFR + SPRL 
Sbjct: 569 SYMNQVRFGNIGNIGSGRNGTGLMLNMAARASVNPVSALSGNMSDNNSSSFRPILSPRLG 628

Query: 598 PVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTL 657
             F GN  Y G     ++   ERGR+RR++++   Q DSKKQ+QL+LEKIR G+DTRTTL
Sbjct: 629 QSFYGNPTYQGPGSFGLDNSIERGRNRRVDSSVF-QADSKKQYQLDLEKIRKGDDTRTTL 687

Query: 658 MIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEA 717
           MIKNIPNKYTSKMLLAAIDE HKGTYDF YLPIDFKNKCNVGYAFINM+SP+HI+ FY+A
Sbjct: 688 MIKNIPNKYTSKMLLAAIDEFHKGTYDFFYLPIDFKNKCNVGYAFINMISPVHIVSFYQA 747

Query: 718 FNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQV 777
           FNGKKWEKFNSEKVASLAYARIQGR AL++HFQNSSLMNEDKRCRPILFHS GP+AG+  
Sbjct: 748 FNGKKWEKFNSEKVASLAYARIQGRTALISHFQNSSLMNEDKRCRPILFHSNGPDAGN-- 805

Query: 778 TQEQLNSNSVNFQVCPSNGSHLRDASGSPIADDEGN 813
            QE    N +   +   +G+    A+G P  ++E N
Sbjct: 806 -QEPFPINGICIHMPLEDGA---IATGDPFGNEEDN 837

Probable RNA-binding protein that may play a role in growth regulation.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8VWF5|AML5_ARATH Protein MEI2-like 5 OS=Arabidopsis thaliana GN=ML5 PE=1 SV=1

 Score =  885 bits (2286), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 493/784 (62%), Positives = 596/784 (76%), Gaps = 46/784 (5%)

Query: 8   SSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDED 67
           SSLPV P  KL L+    G   +DD  + +S+ +    S D  E   + +IGN LPD+ED
Sbjct: 33  SSLPVFPRGKLQLSDNRDGFSLIDD--TAVSRTNKFNESADDFE---SHSIGNLLPDEED 87

Query: 68  ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMS-KISISDSASG 126
            LL G+MDD DL  LP    D +DYD+FGSGGGMEL+ + +++LSMS   ++S+S S  G
Sbjct: 88  -LLTGMMDDLDLGELP----DADDYDLFGSGGGMELDADFRDNLSMSGPPRLSLS-SLGG 141

Query: 127 NGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC 186
           N +  +++PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSEL ALFEQYGDIRTLYT C
Sbjct: 142 NAIPQFNIPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELTALFEQYGDIRTLYTTC 201

Query: 187 KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLD 246
           KHRGFVMISYYDIR+AR AMR+LQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD
Sbjct: 202 KHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKDNPSEKDMNQGTLVVFNLD 261

Query: 247 PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           PS+SN+DL  IFGA+GE+KEIRETPHKRHHKF+EFYDVR AEAALK+LNR +IAGKRIK+
Sbjct: 262 PSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKV 321

Query: 307 EPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPP--GNWVQFSSPIEHNPLQT 364
           EPSRPGGARR+LMLQLNQ+LE D+   L   +GSP+ NSPP  GNW   +SP+E +PLQ+
Sbjct: 322 EPSRPGGARRSLMLQLNQDLENDDLHYLP-MIGSPMANSPPMQGNW-PLNSPVEGSPLQS 379

Query: 365 I-SKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISAN 423
           + S+SP F  +SPT + H+ GLAS L+ Q  +  K+APIG+ Q             I +N
Sbjct: 380 VLSRSPVF-GLSPTRNGHLSGLASALNSQGPS-SKLAPIGRGQ-------------IGSN 424

Query: 424 GASFQQSNS-FSEPKI-GLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSP 481
           G  FQQS+  F EPK+   Y G +S  GP  SNG G+ETLSG +FLWGSP+  SE SSS 
Sbjct: 425 G--FQQSSHLFQEPKMDNKYTGNLSPSGPLISNGGGIETLSGSEFLWGSPNARSEPSSSS 482

Query: 482 AWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPET 541
            W TSS G+P  S      +P+  +  +   S  H HVGSAPSGVPLE+ FGF+PES + 
Sbjct: 483 VWSTSSTGNPLFSTRVDRSVPFPHQHQNQSRSHHHFHVGSAPSGVPLEKHFGFVPESSKD 542

Query: 542 S-FMNPVAFCGM-GIGQNDGSFMVNMGSRASVNPGITVPRNLSDNG-SSFRVMSSPRLSP 598
           + FMN V   GM G+G N GSF   M +   +N G     ++++NG SS+R+MSSPR SP
Sbjct: 543 ALFMNTVGLQGMSGMGLNGGSFSSKMANNGIINSG-----SMAENGFSSYRMMSSPRFSP 597

Query: 599 VFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLM 658
           +FL +G  PG   +  + LYE GR RR+ENN+ NQ++S+KQFQL+LEKI +GED+RTTLM
Sbjct: 598 MFLSSGLNPGRFASGFDSLYENGRPRRVENNS-NQVESRKQFQLDLEKILNGEDSRTTLM 656

Query: 659 IKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAF 718
           IKNIPNKYTSKMLLAAIDE ++GTY+FLYLPIDFKNKCNVGYAFINML+P  IIPFYEAF
Sbjct: 657 IKNIPNKYTSKMLLAAIDEKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAF 716

Query: 719 NGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHS-EGPEAGDQV 777
           NGKKWEKFNSEKVASLAYARIQG++AL+AHFQNSSLMNED RCRPI+F +   PE+ +QV
Sbjct: 717 NGKKWEKFNSEKVASLAYARIQGKSALIAHFQNSSLMNEDMRCRPIIFDTPNNPESVEQV 776

Query: 778 TQEQ 781
             E+
Sbjct: 777 VDEE 780

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVV9|AML3_ARATH Protein MEI2-like 3 OS=Arabidopsis thaliana GN=ML3 PE=2 SV=2

 Score =  797 bits (2059), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/777 (57%), Positives = 548/777 (70%), Gaps = 75/777 (9%)

Query: 11  PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVAS--DDPLEGVMNPAIGNSLPDDEDE 68
           P++ H+  N+N      QSVD+++SGL     G+ +  DD   G  +P IGN LPDDE+E
Sbjct: 28  PLIQHQ--NINPRDSYHQSVDEMASGLDHFSGGIGNMLDD---GDSHP-IGNMLPDDEEE 81

Query: 69  LLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNG 128
           L +G+MDD +L  LP++L+DLEDYD+FGSGGG+ELE +P +SL+   S++  +DS   N 
Sbjct: 82  LFSGLMDDLNLSSLPATLDDLEDYDLFGSGGGLELETDPYDSLNKGFSRMGFADSNVDNV 141

Query: 129 LLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 188
           +      NG G++AGEHPYGEHPSRTLFVRNINSNVEDSEL+ALFEQYG IRTLYTACK 
Sbjct: 142 MPQNIFQNGVGSIAGEHPYGEHPSRTLFVRNINSNVEDSELQALFEQYGHIRTLYTACKQ 201

Query: 189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 248
           RGFVM+SY DIRA+R AMRALQ K L++RKLDIHFSIPKDNPS+KD+NQGTLVVFNL PS
Sbjct: 202 RGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPS 261

Query: 249 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           VSN DL  IFG YGE+KEIRETP+KRHHKF+EF+DVR+A+AALK+LNR++IAGKRIKLE 
Sbjct: 262 VSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADAALKALNRTEIAGKRIKLEH 321

Query: 309 SRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKS 368
           SRPGGARRN+MLQ+N ELEQD+S    + V SP+ +SP GNW   +SPI+H PLQ+ SKS
Sbjct: 322 SRPGGARRNMMLQMNPELEQDDSYSYLNHVESPLASSPIGNWR--NSPIDH-PLQSFSKS 378

Query: 369 PNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQG--RGSLMEHALTNTISANGAS 426
           P F N+SPT         +I +P+ S   K A +  DQ   R S ++H  +++ S N AS
Sbjct: 379 PIFGNLSPTK--------NIRYPEFSM--KTASVNNDQEGRRFSHLDHLFSSS-SYNNAS 427

Query: 427 FQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTS 486
            + S +F +P+      +  S    PS+   VETLSG +FLWGSP       SS AW  +
Sbjct: 428 HKAS-TFQQPQSFGSVSSFGSLNSHPSH---VETLSGSEFLWGSP-------SSSAWPVN 476

Query: 487 SMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNP 546
               PFSSN + H  PYS + GS     Q HH+GSAPS        GF P SPETS M  
Sbjct: 477 ----PFSSNRENHRFPYSAQNGSL---HQLHHIGSAPS--------GFFPRSPETSSMGS 521

Query: 547 VAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGP 605
           VAF G                 AS N  +   RNL +  S +F+++S+PR S +F GNG 
Sbjct: 522 VAFRG-----------------ASGN--MNAQRNLRETSSPNFKMLSAPRRSQLFTGNGS 562

Query: 606 Y--PGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIP 663
           Y  P  T  +I+   E G +++ + +NGNQ D K QFQL+L KI  GED RTTLMIKNIP
Sbjct: 563 YLWPAATMVSIDDPLEDGSNQQFD-SNGNQADIKIQFQLDLSKIMRGEDPRTTLMIKNIP 621

Query: 664 NKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKW 723
           NKYT  MLLAAIDE + GTYDFLYLPIDFKNKCNVGYAFINM+SP   I  YEAFNGKKW
Sbjct: 622 NKYTRNMLLAAIDEKNSGTYDFLYLPIDFKNKCNVGYAFINMVSPKFTIALYEAFNGKKW 681

Query: 724 EKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQE 780
           +KFNSEKVASLAYARIQG+AAL+AHFQNSSLMNED+RC+PI+F  +G E+   + +E
Sbjct: 682 DKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDRRCQPIVF--DGSESKYPIIRE 736

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6EQX3|OML5_ORYSJ Protein MEI2-like 5 OS=Oryza sativa subsp. japonica GN=ML5 PE=2 SV=1

 Score =  738 bits (1906), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 405/778 (52%), Positives = 513/778 (65%), Gaps = 54/778 (6%)

Query: 8   SSLP-VLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDE 66
           SSLP VL   KL         Q  DD+   + +        DP++ V    IGN LPDDE
Sbjct: 49  SSLPSVLQFGKLPGKEREYNAQPKDDMFPMMKQPGTNARVADPMDDVAQHLIGNLLPDDE 108

Query: 67  DELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASG 126
            ELLAG+++DFD   L + +E+ E+YD+F + GGMEL+ +P ES++   +K S+ +  +G
Sbjct: 109 -ELLAGVIEDFDHVKLRTQVEESEEYDVFRNSGGMELDIDPLESITFGTAKASLVN-GTG 166

Query: 127 NGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC 186
           +    YS+ NGAGTV GEHPYGEHPSRTLFVRNINSNVEDSELR+LFE +GDIR++YTA 
Sbjct: 167 SSTNQYSIQNGAGTVTGEHPYGEHPSRTLFVRNINSNVEDSELRSLFEPFGDIRSMYTAT 226

Query: 187 KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLD 246
           KHRGFVMISYYDIR AR A  ALQ+KPLRRRKLDIH+SIPK+NPSDKD+NQGTLV+FNL+
Sbjct: 227 KHRGFVMISYYDIRHARNAKTALQSKPLRRRKLDIHYSIPKENPSDKDMNQGTLVIFNLE 286

Query: 247 PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           P+VSNE+L QIFGA+GEV+EIRETPHKRHH+FIEFYDVRAAE+AL+SLN+SDIAGKR+KL
Sbjct: 287 PAVSNEELLQIFGAFGEVREIRETPHKRHHRFIEFYDVRAAESALRSLNKSDIAGKRVKL 346

Query: 307 EPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTIS 366
           EPSRPGGARR+ +   N E EQDE++    Q+GSP  NSPP  W Q  SP + N L  ++
Sbjct: 347 EPSRPGGARRSFIQHFNHEFEQDETKHNSFQIGSPSANSPPSLWSQLGSPTDENKLNALN 406

Query: 367 KSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGAS 426
           ++     MSP  SNH+ G +S   P  S      P+GK     S   +   + I     +
Sbjct: 407 ETAFNGGMSPLGSNHLSGFSSGYPPMKS------PVGK-----SSYWNNRADNIFHGSPT 455

Query: 427 FQQSNSFSEPKIGLYRGTVSSFGPSPSNGS--GVETLSGPQFLWGSPSRYSEHSSSPAWQ 484
              S+SF E   G+   +      + S  +  G   L+G  FLWG+ +   +H    + Q
Sbjct: 456 LHNSHSFPEHHGGIISASPLVSSAASSASTASGFTALTGTSFLWGNNNNLRDHGQPSSIQ 515

Query: 485 TSSMGHPFSSNGKIHGLP--YSGRQGSFLGSSQHH---HVGSAPSGVPLERRFGFLPESP 539
           + ++ +    N +       Y   +GSF G+S+H    +VGSAPS  P E  FG+  +SP
Sbjct: 516 SQALSNSLFPNNQPQRQSNLYQNLRGSF-GASEHFSQFNVGSAPSVFPFESNFGYFSDSP 574

Query: 540 ETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPV 599
           +TS+M    F G G  +  GS M N G+                          PR++  
Sbjct: 575 DTSYMRQGKFGGTGPTRVSGSLMTNFGAY-------------------------PRINVA 609

Query: 600 FLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMI 659
            + NG          EGL +RGR++ +  N+G Q DS+ Q+QL+LEKI +G+DTRTTLMI
Sbjct: 610 SMQNGS------VGFEGLLDRGRNQTV-GNSGCQEDSRVQYQLDLEKIIAGKDTRTTLMI 662

Query: 660 KNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFN 719
           KNIPNKYTS MLL  IDE H+GTYDF YLPIDFKNKCNVGYAFINM SP +I+ F++AF 
Sbjct: 663 KNIPNKYTSNMLLEVIDETHEGTYDFFYLPIDFKNKCNVGYAFINMASPGYIVSFFKAFA 722

Query: 720 GKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQV 777
           G+KWEKFNSEKV SLAYARIQG+AALV HFQNSSLMNEDKRCRP+LF  +  E  +Q+
Sbjct: 723 GRKWEKFNSEKVVSLAYARIQGKAALVNHFQNSSLMNEDKRCRPMLFDPKHTENNNQI 780

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SJG8|AML2_ARATH Protein MEI2-like 2 OS=Arabidopsis thaliana GN=ML2 PE=2 SV=2

 Score =  671 bits (1732), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/803 (47%), Positives = 507/803 (63%), Gaps = 35/803 (4%)

Query: 10  LPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDEL 69
           LP L HEKLN+        S D+ S  L+K+  G +  D LE V   A+   LP+DE+EL
Sbjct: 56  LPTLFHEKLNMTDSD-SWLSFDESSPNLNKLVIGNSEKDSLEDVEPDALEILLPEDENEL 114

Query: 70  LAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGL 129
           L G++D+ +  GLP  L+DLE+ D+F +GGGMEL+ E Q++ ++  S + ISD  + N  
Sbjct: 115 LPGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVESQDNHAVDASGMQISDRGAANAF 174

Query: 130 LHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR 189
           +    PN AG V+ EHP GEHPSRTLFVRNINS+VEDSEL ALFE +G+IR+LYTACK R
Sbjct: 175 VPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVEDSELSALFEPFGEIRSLYTACKSR 234

Query: 190 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV 249
           GFVMISYYDIRAA  AMRALQN  LR+R LDIHFSIPK+NPS+KD+NQGTLV+FN+D +V
Sbjct: 235 GFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDTTV 294

Query: 250 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 309
           SN++L Q+FGAYGE++EIRETP++R H+FIE+YDVR AE ALK+LNRS+I GK IKLE S
Sbjct: 295 SNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLELS 354

Query: 310 RPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSP 369
           RPGGARR  +   +Q+LE+ E     +QVGS + NSPPGNW    SP++ +P    ++  
Sbjct: 355 RPGGARRLSVPSQSQDLERTEVTNFYNQVGSHVANSPPGNW-PIGSPVKGSPSHAFTRPH 413

Query: 370 NFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQ 429
               + P  S++MPGLASIL    S+    +P+  DQG  +     + N    +  S+ Q
Sbjct: 414 GLGMVRPVNSDNMPGLASILPAHPSSFHGFSPVSNDQGLLNHSNQTILNKGLMHNISYGQ 473

Query: 430 SNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQ----- 484
            +S  E   G    ++    P   + SG  T S  ++ WGSP    +H + P +      
Sbjct: 474 PHSLPEHITGGISNSMRFIAP---HSSGFGTSSDHRYRWGSP---PQHMNYPGYTGVSSS 527

Query: 485 TSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFM 544
           +SS   PF+     HG P++ RQ S LG  Q HHVGSAPS +    +      SPE    
Sbjct: 528 SSSTERPFTVR---HGFPFAERQASLLGKYQ-HHVGSAPSSIHFNTQMNCYTGSPEI--- 580

Query: 545 NPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNG 604
            P+ F  MGI +N  S      +    N G+++P N S+   +   MSS    P     G
Sbjct: 581 -PLGFSDMGINRNYNS------AHGKANLGVSLPGNSSEQDFTGFGMSSMPTVPF----G 629

Query: 605 PYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPN 664
              GL     E   E+GR    E++N NQ     ++ ++L++I SG++ RTTL+IKNIPN
Sbjct: 630 GSRGLQSVRPEPFAEQGRIHNHESHNQNQFIDGGRYHIDLDRIASGDEIRTTLIIKNIPN 689

Query: 665 KYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWE 724
           KYT KML+A IDE HKG YDFL LP DFKNKCN+G+AFINM+SPLHI+PF + FNGK WE
Sbjct: 690 KYTYKMLVAEIDEKHKGDYDFLCLPTDFKNKCNMGHAFINMVSPLHIVPFQQTFNGKIWE 749

Query: 725 KFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRP-ILFHSEGPEAGDQVTQEQLN 783
           KFNS KVASLAYA IQG++AL ++ Q  S M E K+  P + +H +G +A D    EQL 
Sbjct: 750 KFNSGKVASLAYAEIQGKSALASYMQTPSSMKEQKQLFPEVSYHDDGQDAND---HEQLF 806

Query: 784 SNSVNFQVCPSNGSHLRDASGSP 806
           S+  N     S+ S+  D   +P
Sbjct: 807 SSIWNITAPDSDWSYTMDLIENP 829

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q75M35|OML3_ORYSJ Protein MEI2-like 3 OS=Oryza sativa subsp. japonica GN=ML3 PE=2 SV=2

 Score =  479 bits (1234), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 333/804 (41%), Positives = 437/804 (54%), Gaps = 109/804 (13%)

Query: 24  GLGRQSVDDISSGLSKVHHGVA-SDDPLE---GVMNPAIGNSLPDDEDELLAGIMDDFDL 79
           G  R+ V  +    +  H  +  SD+PLE    +    IG+ LPDD+D+L++GI D F+ 
Sbjct: 156 GKSREIVSGVLCQSTGTHTSIYDSDEPLESMEAIEAQTIGDLLPDDDDDLISGIADGFEF 215

Query: 80  RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 139
            G+ S+ +D  D DIF +GGGMELE                +DS  G+ +   S  +   
Sbjct: 216 TGM-STNQDDADEDIFCTGGGMELEN---------------NDSVKGDKVQDGSFKS--- 256

Query: 140 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 199
            ++  H   + PSRTL VRNI +N+EDS+L  LF+QYGDIR LYT+ KH GFV +SYYDI
Sbjct: 257 QISSGHSINKQPSRTLVVRNITANIEDSDLTVLFQQYGDIRMLYTSFKHHGFVTVSYYDI 316

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 259
           RAA+ AMRAL +KPL   KLD+ FS PK+N   KD+++G LVV N+D S+SN+DL Q+  
Sbjct: 317 RAAQNAMRALHSKPLGLMKLDVQFSFPKENVPGKDIDKGMLVVSNIDSSISNDDLLQMLS 376

Query: 260 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 319
            YG+VKEI  +P     KF+EFYDVRAAE AL  LN+  I+G + K+E S+ G A   L 
Sbjct: 377 VYGDVKEISSSPISCTKKFVEFYDVRAAEEALHDLNKGGISGPKFKVELSQHGEAGSCLR 436

Query: 320 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHN-PLQTISKSPNFRNMSPTT 378
            Q ++E +QD    L HQ      NS PG   +  +  + N  +  +    N +  SPT 
Sbjct: 437 QQHSREWKQDS---LPHQP----KNSSPGTIGKLGTKCQDNSTVHNLFSPVNQQLESPTQ 489

Query: 379 SNHMPGLASILHP-----------QVSTLEKIAPIGKDQ-GRG-------SLMEHALTNT 419
                G   +  P           Q S  +   P+G+   GRG       SL EH   N 
Sbjct: 490 CISTTGPQILSSPIRIKSTLQHNNQASVGDLSGPLGQGNFGRGIQTLHPRSLPEHH--NR 547

Query: 420 ISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVET--------------LSGPQ 465
           I  N  S   S   +  +       +   GP+   G   +               L G  
Sbjct: 548 ICNNSKSMTVSGRNASSRQDGVDHNIQKVGPAGFCGHSFDQNNEAFGFTEIGSCPLHGYH 607

Query: 466 FLWGSPSRYSEHSSSPA-WQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPS 524
           + W   + + +  S+P  W  S++ HP   +      P+    GS+      HH+GSAP 
Sbjct: 608 YTWNHTNVFPQSPSAPILW--SNLQHPMHVHSYPGVPPHMLNTGSY--PMDQHHLGSAPD 663

Query: 525 GVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDN 584
                            SF N  +F    +G        ++G   S  P +  P  LS  
Sbjct: 664 N--------------GGSFGNVHSFHPGSLG--------SIGLHGS--PQL-YPSELSAF 698

Query: 585 GSSFRVMSSPRLSPVFLG-----------NGPYPGL-TPANIEGLYERGRSRRIENNNGN 632
            SS         SPV  G           NG  P +    + +   +R RSRR  + N  
Sbjct: 699 ASSRGNFREALFSPVGGGFQSLQQMCNAINGRNPMIHVSTSYDATNDRMRSRR-HDGNPA 757

Query: 633 QLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDF 692
           Q ++K+QF+L++++I  GED+RTTLMIKNIPNKY  K+LLA IDENH+GTYDF+YLPIDF
Sbjct: 758 QSENKRQFELDIDRIAKGEDSRTTLMIKNIPNKYNCKLLLAVIDENHRGTYDFIYLPIDF 817

Query: 693 KNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNS 752
           KNKCNVGYAFINM  P HIIPFY+ FNGKKWEKFNSEKVASLAYARIQGR+AL+AHFQNS
Sbjct: 818 KNKCNVGYAFINMTDPQHIIPFYKTFNGKKWEKFNSEKVASLAYARIQGRSALIAHFQNS 877

Query: 753 SLMNEDKRCRPILFHSEGPEAGDQ 776
           SLMNEDK CRP+LFH +GP AGDQ
Sbjct: 878 SLMNEDKWCRPMLFHKDGPNAGDQ 901

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q64M78|OML4_ORYSJ Protein MEI2-like 4 OS=Oryza sativa subsp. japonica GN=ML4 PE=2 SV=1

 Score =  296 bits (757), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 171/323 (52%), Positives = 210/323 (65%), Gaps = 19/323 (5%)

Query: 465 QFLWGSPSRYSEHSSSPAWQTSSMGH----PFSSNGKIHGLPY--SGRQGSFLGSSQHHH 518
           Q +W + S +  H +SP    S        P  S  ++HG+P   S      +    H H
Sbjct: 637 QLMWNNSSNFHHHPNSPVLWPSPGSFVNNVPSRSPAQMHGVPRAPSSHMIDNVLPMHHLH 696

Query: 519 VGSAPSGVP--LERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGIT 576
           VGSAP+  P   +RR G+  E  E    +P +   MG     GS  ++     ++ P   
Sbjct: 697 VGSAPAINPSLWDRRHGYAGELTEAPNFHPGSVGSMGF---PGSPQLHSMELNNIYP--Q 751

Query: 577 VPRNLSDNGSSFRVMSSP---RLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQ 633
              N  D   S   +  P   +   +F G  P   L   +  G  ER RSRR  ++NGNQ
Sbjct: 752 TGGNCMDPTVSPAQIGGPSPQQRGSMFHGRNPMVPLPSFDSPG--ERMRSRR-NDSNGNQ 808

Query: 634 LDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFK 693
            D+KKQ++L++++I  G+D+RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDF+YLPIDFK
Sbjct: 809 SDNKKQYELDVDRIVRGDDSRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFIYLPIDFK 868

Query: 694 NKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSS 753
           NKCNVGYAFINM +P HIIPFY+ FNGKKWEKFNSEKVASLAYARIQG++AL+AHFQNSS
Sbjct: 869 NKCNVGYAFINMTNPQHIIPFYQTFNGKKWEKFNSEKVASLAYARIQGKSALIAHFQNSS 928

Query: 754 LMNEDKRCRPILFHSEGPEAGDQ 776
           LMNEDKRCRPILFHS+GP AGDQ
Sbjct: 929 LMNEDKRCRPILFHSDGPNAGDQ 951

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LYN7|AML4_ARATH Protein MEI2-like 4 OS=Arabidopsis thaliana GN=ML4 PE=1 SV=1

 Score =  273 bits (698), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 152/267 (56%), Positives = 189/267 (70%), Gaps = 12/267 (4%)

Query: 516 HHHVGSAPS-GVPL-ERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNP 573
           HHH+GSAP    P  +RR  ++ ESPE+S  +  +   MG   +  S  ++ GS    + 
Sbjct: 603 HHHIGSAPVLNSPFWDRRQAYVAESPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKVFS- 661

Query: 574 GITVPRNLSDNGSSFRVMSSPRLSP-VFLGNGPYPGLTPANIEGLYERGRS---RRIENN 629
              V  N  +  S   V+ S R  P +F G  P   ++  + +   ER R+   RR E+N
Sbjct: 662 --HVGGNRMEANSKNAVLRSSRQMPHLFTGRSPMLSVS-GSFDLPNERYRNLSHRRSESN 718

Query: 630 NGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP 689
           + N    KK ++L++++I  GED+RTTLMIKNIPNKYTSKMLLAAIDE  KGTYDFLYLP
Sbjct: 719 SSNA--EKKLYELDVDRILRGEDSRTTLMIKNIPNKYTSKMLLAAIDEYCKGTYDFLYLP 776

Query: 690 IDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHF 749
           IDFKNKCNVGYAFIN++ P +I+PFY+AFNGKKWEKFNSEKVASLAY RIQG++AL+AHF
Sbjct: 777 IDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAYGRIQGKSALIAHF 836

Query: 750 QNSSLMNEDKRCRPILFHSEGPEAGDQ 776
           QNSSLMNEDKRCRPILFH+ GP AGDQ
Sbjct: 837 QNSSLMNEDKRCRPILFHTAGPNAGDQ 863

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W4I9|AML1_ARATH Protein MEI2-like 1 OS=Arabidopsis thaliana GN=ML1 PE=1 SV=1

 Score =  228 bits (582), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 128/259 (49%), Positives = 172/259 (66%), Gaps = 19/259 (7%)

Query: 57  AIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMS 116
            IGN LPD ED+L A +  +   +   ++ ++L+++D+F S GGMEL+G+   S+S    
Sbjct: 140 TIGNLLPD-EDDLFAEVTGEVGRKSRANTGDELDEFDLFSSVGGMELDGDIFSSVS---- 194

Query: 117 KISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQY 176
                         H +   G     GE   GE PSRTL V NI+SNVED EL+ LFEQ+
Sbjct: 195 --------------HRNGERGGNNSVGELNRGEIPSRTLLVGNISSNVEDYELKVLFEQF 240

Query: 177 GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN 236
           GDI+ L+TACK+RGF+M+SY DIRAA+ A RALQNK LR  KLDI +SI K+NPS KD +
Sbjct: 241 GDIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDTS 300

Query: 237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           +G L+V NLD S+SN++L ++  +YGEVKEIR T H     +IEF+DVRAA AAL  LN 
Sbjct: 301 KGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLNG 360

Query: 297 SDIAGKRIKLEPSRPGGAR 315
            ++AGK+++L P+ P G R
Sbjct: 361 LEVAGKKLQLVPTYPEGTR 379

Probable RNA-binding transcriptional activator that plays a role in meiosis and vegetative growth. May be a downstream effector of TOR signaling pathway and recruited by RAPTOR1 for TOR substrate.

Arabidopsis thaliana (taxid: 3702)

>sp|P08965|MEI2_SCHPO Meiosis protein mei2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mei2 PE=1 SV=1

 Score =  155 bits (393), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 73/133 (54%), Positives = 94/133 (70%)

Query: 642 LELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYA 701
           ++  +I SG DTRTT+MIKNIPNK+T +ML   ID  +KGTYDFLYL IDF NKCNVGYA
Sbjct: 584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query: 702 FINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRC 761
           FIN + P  II F +A  G +W  F+SEK+  ++YA IQG+  L+  F+NS +M+E+   
Sbjct: 644 FINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQGKDRLIEKFRNSCVMDENPAY 703

Query: 762 RPILFHSEGPEAG 774
           RP +F S GP  G
Sbjct: 704 RPKIFVSHGPNRG 716

Crucial for commitment to meiosis but it is not sufficient itself for the commitment. May be a splicing regulator.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	818
47834701	858	AML1 [Citrus unshiu]	0.991	0.945	0.991	0.0
225463378	860	PREDICTED: protein MEI2-like 2-like [Vit	0.986	0.938	0.772	0.0
356556525	862	PREDICTED: protein MEI2-like 2-like [Gly	0.968	0.918	0.757	0.0
356530557	862	PREDICTED: protein MEI2-like 2-like [Gly	0.968	0.918	0.749	0.0
359485142	842	PREDICTED: protein MEI2-like 2-like [Vit	0.959	0.932	0.716	0.0
357450609	865	Polyadenylate-binding protein [Medicago	0.965	0.913	0.717	0.0
297740630	787	unnamed protein product [Vitis vinifera]	0.871	0.905	0.691	0.0
357450611	764	Polyadenylate-binding protein [Medicago	0.903	0.967	0.731	0.0
356567420	857	PREDICTED: protein MEI2-like 2-like [Gly	0.963	0.919	0.690	0.0
255586946	779	RNA-binding protein, putative [Ricinus c	0.915	0.961	0.707	0.0

>gi|47834701|gb|AAT39004.1| AML1 [Citrus unshiu]

 Score = 1654 bits (4283), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 804/811 (99%), Positives = 810/811 (99%)

Query: 8   SSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDED 67
           SSLPVLPHEKLNLNAMGLGRQSVD+ISSGLSKVHHGV+SDDPLEG+MNPAIGNSLPDDED
Sbjct: 48  SSLPVLPHEKLNLNAMGLGRQSVDNISSGLSKVHHGVSSDDPLEGIMNPAIGNSLPDDED 107

Query: 68  ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN 127
           ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN
Sbjct: 108 ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN 167

Query: 128 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 187
           GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK
Sbjct: 168 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 227

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 247
           HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP
Sbjct: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 287

Query: 248 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
           SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE
Sbjct: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347

Query: 308 PSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISK 367
           PSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISK
Sbjct: 348 PSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISK 407

Query: 368 SPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASF 427
           SPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASF
Sbjct: 408 SPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASF 467

Query: 428 QQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSS 487
           QQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSS
Sbjct: 468 QQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSS 527

Query: 488 MGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPV 547
           MGHPFSSNGKIHGLPYSGRQGSFLGSSQHHH+GSAPSGVPLERRFGFLPESPETSFMNPV
Sbjct: 528 MGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHIGSAPSGVPLERRFGFLPESPETSFMNPV 587

Query: 548 AFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYP 607
           AFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYP
Sbjct: 588 AFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYP 647

Query: 608 GLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYT 667
           GLTPAN EGLYERGRSRRIENNNGNQ+DSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYT
Sbjct: 648 GLTPANSEGLYERGRSRRIENNNGNQIDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYT 707

Query: 668 SKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN 727
           SKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN
Sbjct: 708 SKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN 767

Query: 728 SEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSV 787
           SEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNS+SV
Sbjct: 768 SEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSDSV 827

Query: 788 NFQVCPSNGSHLRDASGSPIADDEGNKPENS 818
           NFQVCPSNGSHLRDASGSPIADDEGNKPENS
Sbjct: 828 NFQVCPSNGSHLRDASGSPIADDEGNKPENS 858

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463378|ref|XP_002271605.1| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]

 Score = 1264 bits (3270), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 629/814 (77%), Positives = 702/814 (86%), Gaps = 7/814 (0%)

Query: 9   SLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDE 68
           SLPVLPHEKLNLN      QS+DD  +GL K+   V + + LE     AIG+ LPDDEDE
Sbjct: 50  SLPVLPHEKLNLNDTEHCCQSIDD--AGLDKLQQDVEAGESLEDDGIHAIGSLLPDDEDE 107

Query: 69  LLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNG 128
           LLAGIMDDFDL GL + +ED+E+YD+FGSGGGMELE +PQESL+M M+K+S+SD   GNG
Sbjct: 108 LLAGIMDDFDLSGLSNPMEDVEEYDLFGSGGGMELEIDPQESLNMGMAKVSLSDGVVGNG 167

Query: 129 LLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 188
           L  Y +PNG+GTVAGEHPYGEHPSRTLFVRNINSNVEDSELR LFEQYG IRTLYTACKH
Sbjct: 168 LAQYGLPNGSGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRTLFEQYGAIRTLYTACKH 227

Query: 189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 248
           RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPS
Sbjct: 228 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDVNQGTLVVFNLDPS 287

Query: 249 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           VSN+DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAAL+SLNRSDIAGKRIKLEP
Sbjct: 288 VSNDDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALRSLNRSDIAGKRIKLEP 347

Query: 309 SRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKS 368
           SRPGGARRNLMLQLNQELEQDESR  +H VGSP+ NSPPG+W QFSSPIEH+PLQ++SKS
Sbjct: 348 SRPGGARRNLMLQLNQELEQDESRSFRHHVGSPMANSPPGSWAQFSSPIEHSPLQSLSKS 407

Query: 369 PNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQ 428
           P FR +SPTTSNH+PGLASIL+ Q+S   K+APIGKDQGRG  +E+   NT S +G +FQ
Sbjct: 408 PGFRTVSPTTSNHLPGLASILNSQISNSVKVAPIGKDQGRGIHVENIFNNTNSNHGTAFQ 467

Query: 429 QSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSM 488
           QS+SFSEP +G Y G  SSFG S SNGSG+ETLSGPQFLWGSP+ YSEH++S AWQ  SM
Sbjct: 468 QSHSFSEPNLGPYPGNGSSFGASTSNGSGIETLSGPQFLWGSPAPYSEHTNSSAWQPPSM 527

Query: 489 GHPFSSNGKIHGLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMN 545
           GHPF+SNG+  G PYSGR GSFLGSS+   HHHVGSAPSGVPLER FG+ PESPE SFM 
Sbjct: 528 GHPFASNGQGRGFPYSGRHGSFLGSSRHHHHHHVGSAPSGVPLERHFGYFPESPEASFMT 587

Query: 546 PVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNG 604
           PVAF GMG+  NDGSFM+NM +RA +N GI++P N+S++GS+ FR++SSPRLSP+F GNG
Sbjct: 588 PVAFGGMGLAHNDGSFMLNMSARAGMNAGISIPANMSESGSANFRMISSPRLSPMFPGNG 647

Query: 605 PYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPN 664
           P+PGL P+NIEGL +RGRSR +E NNGNQ+DSKKQFQL+L+KI +GEDTRTTLMIKNIPN
Sbjct: 648 PFPGLAPSNIEGLADRGRSRWVE-NNGNQIDSKKQFQLDLDKILNGEDTRTTLMIKNIPN 706

Query: 665 KYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWE 724
           KYTSKMLLAAIDE H+GTYDFLYLPIDFKNKCNVGYAFINMLSP HIIPFY+AFNGKKWE
Sbjct: 707 KYTSKMLLAAIDEYHRGTYDFLYLPIDFKNKCNVGYAFINMLSPSHIIPFYQAFNGKKWE 766

Query: 725 KFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNS 784
           KFNSEKVASLAYARIQG+AALV HFQNSSLMNEDKRCRPILFHSEGPEAGDQ+ QE L S
Sbjct: 767 KFNSEKVASLAYARIQGKAALVTHFQNSSLMNEDKRCRPILFHSEGPEAGDQIIQEHLPS 826

Query: 785 NSVNFQVCPSNGSHLRDASGSPIADDEGNKPENS 818
           NS+N QV   NGS + D   SP       KPE S
Sbjct: 827 NSLNIQVPQPNGSQIGDTPESPEMVLLCEKPEKS 860

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556525|ref|XP_003546575.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1214 bits (3141), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 608/803 (75%), Positives = 671/803 (83%), Gaps = 11/803 (1%)

Query: 11  PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELL 70
           PVLPHEKLNLN    G QS+DDISSG  K+H     +  LE     AIG +LPDDE+ELL
Sbjct: 52  PVLPHEKLNLNETANGYQSIDDISSGFKKLHQDADGNGSLEDGDTHAIGPALPDDEEELL 111

Query: 71  AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLL 130
           AGI DDFDL GLP SLEDLE+YD+FGSGGGMELE +PQE L++ +SK+S +DS  GNGL 
Sbjct: 112 AGITDDFDLSGLPGSLEDLEEYDLFGSGGGMELETDPQEGLTVGLSKLSFADSTVGNGLP 171

Query: 131 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 190
            YS PNG GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG
Sbjct: 172 PYSFPNGVGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 231

Query: 191 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVS 250
           FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVS
Sbjct: 232 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVS 291

Query: 251 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 310
           NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR
Sbjct: 292 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 351

Query: 311 PGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPN 370
           PGGARRNLMLQLNQEL+QDESR  ++QVGSP+ NSPPGNW+QF+SP+E N +QTI+ SP 
Sbjct: 352 PGGARRNLMLQLNQELDQDESRSFRYQVGSPVANSPPGNWLQFNSPVEQNSMQTINYSPG 411

Query: 371 FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQS 430
            R +SPTT NH+PGLASIL PQVS   K A IG D  R S  EH  T   S++GA+F QS
Sbjct: 412 SRIISPTTGNHLPGLASILQPQVSNTVKAAAIGNDLERSSQGEHIFTGMNSSHGATF-QS 470

Query: 431 NSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGH 490
           +S  EPK   YRG +SS GPS SNGS VETLSGPQFLWGSP+ YSEH+   AW  SS+GH
Sbjct: 471 HSLPEPKFSQYRGALSSIGPSTSNGSSVETLSGPQFLWGSPTLYSEHTKPSAWPRSSVGH 530

Query: 491 PFSSNGKIHGLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPV 547
           PF+SNGK H  PYS +  SF+GSSQ   HHHVGSAPSG+P ER FGF PES ETSFMN V
Sbjct: 531 PFASNGKSHAFPYSTQNSSFVGSSQHLHHHHVGSAPSGLPFERHFGFHPESSETSFMNNV 590

Query: 548 AFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPY 606
            + G+G G NDG+ MVN+G   SVNP IT+PRN+SDNGSS FR+ SSPRLSPVFLGNGP+
Sbjct: 591 GYGGIGPGHNDGNHMVNVG--GSVNPNITIPRNISDNGSSNFRMRSSPRLSPVFLGNGPF 648

Query: 607 PGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKY 666
           PGL P  +EGL +R RSR IE NNG+Q+DSKKQFQL L+KI+SGEDTRTTLMIKNIPNKY
Sbjct: 649 PGLPPTTLEGLADRARSRWIE-NNGSQVDSKKQFQLNLDKIKSGEDTRTTLMIKNIPNKY 707

Query: 667 TSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKF 726
           TSKMLLAAIDENH+GTYDFLYLPIDFKNKCNVGYAFINMLSP  IIPF+E FNGKKWEKF
Sbjct: 708 TSKMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIPFFETFNGKKWEKF 767

Query: 727 NSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQ---LN 783
           NSEKVASLAYARIQG++ALV+HFQNSSLMNEDKRCRPILFHSEG E  D + Q+     N
Sbjct: 768 NSEKVASLAYARIQGKSALVSHFQNSSLMNEDKRCRPILFHSEGSEVCDLIVQDHHLPSN 827

Query: 784 SNSVNFQVCPSNGSHLRDASGSP 806
           SN++N Q    +  +  D +GSP
Sbjct: 828 SNNLNIQAPRPSEFYSSDFAGSP 850

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530557|ref|XP_003533847.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1195 bits (3092), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 602/803 (74%), Positives = 667/803 (83%), Gaps = 11/803 (1%)

Query: 11  PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELL 70
           PVLPHEKLNLN      QS+DDISSG  K+H     +  LE     AIG +LPDDE+ELL
Sbjct: 52  PVLPHEKLNLNETANAYQSIDDISSGFKKLHQDAEGNGSLEDGDTHAIGPALPDDEEELL 111

Query: 71  AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLL 130
           AGIMDDFDL GLP SLEDLE+YD+FG GGGMELE +PQESL++ +SK+S +DS  G+ L 
Sbjct: 112 AGIMDDFDLSGLPGSLEDLEEYDLFGCGGGMELETDPQESLTVGISKLSFADSTVGSVLP 171

Query: 131 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 190
            YS PNG G VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG
Sbjct: 172 PYSFPNGVGAVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 231

Query: 191 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVS 250
           FVMISYYDIRAARTAMR+LQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVS
Sbjct: 232 FVMISYYDIRAARTAMRSLQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVS 291

Query: 251 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 310
           NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR
Sbjct: 292 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 351

Query: 311 PGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPN 370
           PGGARRNLMLQLNQEL+Q+ESR  ++QV SP+ NSPPGNW+QF+SP+E N +QTI+ SP 
Sbjct: 352 PGGARRNLMLQLNQELDQEESRSFRYQVSSPVANSPPGNWLQFNSPVEQNSMQTINHSPG 411

Query: 371 FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQS 430
            R +SPTT NH+PGLASIL PQVS   K A IG D GR S  EH  +   S++GA+F QS
Sbjct: 412 SRIISPTTGNHLPGLASILQPQVSNAVKAAAIGNDLGRSSQGEHIFSGMNSSHGATF-QS 470

Query: 431 NSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGH 490
           +S  EPK   YRG +SS GPS SNGS VETLSGPQFLWGSP+ YSEH+    W  SS+GH
Sbjct: 471 HSLPEPKFSQYRGALSSIGPSTSNGSSVETLSGPQFLWGSPTLYSEHTKPSVWPRSSVGH 530

Query: 491 PF-SSNGKIHGLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNP 546
           PF +SNGK H  PYS +  SF+GSSQ   HHHVGSAPSG+P ER FGF PES ETSFMN 
Sbjct: 531 PFAASNGKSHAFPYSTQNSSFVGSSQHHHHHHVGSAPSGLPFERHFGFHPESSETSFMNN 590

Query: 547 VAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGP 605
           V + G+G+G NDG++MVN G   SVNP  T+PRN+SDNGSS  R+ SSPRLSPVFLGNGP
Sbjct: 591 VGYGGIGLGHNDGNYMVNAG--GSVNPNTTIPRNISDNGSSNLRMRSSPRLSPVFLGNGP 648

Query: 606 YPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNK 665
           YPGL P  +E L +R RSR IE NNG+Q+DSKKQFQL+L+KIRSGEDTRTTLMIKNIPNK
Sbjct: 649 YPGLPPTTLESLADRARSRWIE-NNGSQVDSKKQFQLDLDKIRSGEDTRTTLMIKNIPNK 707

Query: 666 YTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEK 725
           YTSKMLLAAIDENH+G YDFLYLPIDFK KCNVGYAFINMLSP  IIPFYE FNGKKWEK
Sbjct: 708 YTSKMLLAAIDENHRGAYDFLYLPIDFKKKCNVGYAFINMLSPFLIIPFYETFNGKKWEK 767

Query: 726 FNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQL--N 783
           FNSEKVASLAYARIQG++ALV+HFQNSSLMNEDKRCRPILFHSEG E GD + QE L  N
Sbjct: 768 FNSEKVASLAYARIQGKSALVSHFQNSSLMNEDKRCRPILFHSEGSEVGDLIVQEHLSSN 827

Query: 784 SNSVNFQVCPSNGSHLRDASGSP 806
           SN++N Q    +  +  D +GSP
Sbjct: 828 SNNLNIQAPRPSEFYSSDFAGSP 850

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485142|ref|XP_002279792.2| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]

 Score = 1124 bits (2906), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 572/798 (71%), Positives = 652/798 (81%), Gaps = 13/798 (1%)

Query: 10  LPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDEL 69
           LPVLPHEKL+ N       SVDD S  L+K+     S DPLE V   AIG+ LPDDEDEL
Sbjct: 51  LPVLPHEKLHFNDSEHCGHSVDDGSPSLNKLQQDEESKDPLEDVDLNAIGSLLPDDEDEL 110

Query: 70  LAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGL 129
           LAGIMDDFDL GLP+ +EDLED D+FGSGGGMEL+        + +SK+S+SD  +GNG+
Sbjct: 111 LAGIMDDFDLSGLPTQVEDLED-DLFGSGGGMELD------FDIGISKLSLSDGVAGNGI 163

Query: 130 LHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR 189
            HY +PNG  TVAGEHPYGEHPSRTLFVRNINSNVEDSEL+ LFEQYGDIRTLYTACKHR
Sbjct: 164 GHYGLPNGVATVAGEHPYGEHPSRTLFVRNINSNVEDSELKTLFEQYGDIRTLYTACKHR 223

Query: 190 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV 249
           GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD SV
Sbjct: 224 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDASV 283

Query: 250 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 309
           SN+DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAAL++LNRSDIAGKRIKLEPS
Sbjct: 284 SNDDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALRALNRSDIAGKRIKLEPS 343

Query: 310 RPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSP 369
           RPGGARRNLM QL+QELEQDE+R  +H VGSP+TNSPPGNW  F SP+EHNPLQ  S SP
Sbjct: 344 RPGGARRNLMQQLSQELEQDEARSFRHHVGSPVTNSPPGNWAAF-SPVEHNPLQAYSHSP 402

Query: 370 NFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQ 429
              N+SP  SNH+PGLASIL P +S   KIAPIGKDQGR + +    TN     GA++Q 
Sbjct: 403 GLGNISPINSNHLPGLASILPPHISNSVKIAPIGKDQGRVNHVNQVFTNAKPTQGAAYQI 462

Query: 430 SNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMG 489
           S+S  E K+    G +SS G S SN SG+ TLSGPQFLWGSP+ YSE  +S AW TSS+G
Sbjct: 463 SHSVPEQKLSASPGPISSLGESNSNSSGIGTLSGPQFLWGSPTPYSERPNSSAWPTSSVG 522

Query: 490 HPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAF 549
           HPF S+G+  G PYS + GSFLGS QHHHVGSAPSGVPL+R FG+ PESPETSFM+PV F
Sbjct: 523 HPFVSSGQGQGFPYSNQHGSFLGSHQHHHVGSAPSGVPLDRHFGYFPESPETSFMSPVTF 582

Query: 550 CGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNG-SSFRVMSSPRLSPVFLGNGPYPG 608
            GMG+ +++G+F +N+G+RA++N G+ +P N+++NG  SFR++S PR  P FLGNG YP 
Sbjct: 583 GGMGLSRSNGNFAMNVGARAAINTGVALPGNMTENGLPSFRMLSLPRHGPPFLGNGTYPV 642

Query: 609 LTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTS 668
               + E L ERGR+RR+E N+GNQ+DSKKQ+QL+L+KI SGEDTRTTLMIKNIPNKYTS
Sbjct: 643 SGVTSNEVLAERGRTRRVE-NSGNQIDSKKQYQLDLDKIISGEDTRTTLMIKNIPNKYTS 701

Query: 669 KMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNS 728
           KMLLAAIDENH+GTYDFLYLPIDFKNKCNVGYAFINM+SP HIIPFYEAFNGKKWEKFNS
Sbjct: 702 KMLLAAIDENHRGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIIPFYEAFNGKKWEKFNS 761

Query: 729 EKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVN 788
           EKVASLAYARIQG+AALV HFQNSSLMNEDKRCRPILFHSEG E    V QE   S ++N
Sbjct: 762 EKVASLAYARIQGKAALVTHFQNSSLMNEDKRCRPILFHSEGQET---VDQEPFASGNLN 818

Query: 789 FQVCPSNGSHLRDASGSP 806
             +   +GS+  D+  SP
Sbjct: 819 ICIRQPDGSYSGDSLESP 836

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450609|ref|XP_003595581.1| Polyadenylate-binding protein [Medicago truncatula] gi|47834691|gb|AAT38999.1| AML5 [Medicago truncatula] gi|87241360|gb|ABD33218.1| RNA-binding region RNP-1 (RNA recognition motif); RNA recognition motif 2 [Medicago truncatula] gi|355484629|gb|AES65832.1| Polyadenylate-binding protein [Medicago truncatula]

 Score = 1120 bits (2896), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 577/804 (71%), Positives = 649/804 (80%), Gaps = 14/804 (1%)

Query: 11  PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELL 70
           PVLPHEKLNLN    G QSVDDIS+   K H     +  L+   N AIG  LPDD++ELL
Sbjct: 52  PVLPHEKLNLNETENGFQSVDDISTNFKKHHQEAELNGSLDNGNNHAIGTMLPDDDEELL 111

Query: 71  AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLL 130
           AGIMDDFDLRGLP SLEDLE+YD+F S GG+ELE +PQESLS+ +SK+S+SDS+ GN + 
Sbjct: 112 AGIMDDFDLRGLPGSLEDLEEYDLFDSSGGLELETDPQESLSVGISKLSLSDSSVGNSMP 171

Query: 131 HYSVPNGAGTVAG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 188
            YS+PNG G  A   EHPYGEHPSRTLFVRNINSNVED+ELR LFEQYGDIRTLYTACKH
Sbjct: 172 PYSLPNGVGGGAVAGEHPYGEHPSRTLFVRNINSNVEDTELRTLFEQYGDIRTLYTACKH 231

Query: 189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 248
           RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPS
Sbjct: 232 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPS 291

Query: 249 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE+YDVRAAEAALKSLNRSDIAGKRIKLEP
Sbjct: 292 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEYYDVRAAEAALKSLNRSDIAGKRIKLEP 351

Query: 309 SRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKS 368
           SRPGGARRNLMLQLNQEL+QDESR  ++QVGSP+  SPPGNW+QF+SPIE + L  ++ S
Sbjct: 352 SRPGGARRNLMLQLNQELDQDESRSFRYQVGSPLAGSPPGNWLQFNSPIEQSSLPNLNHS 411

Query: 369 PNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQ 428
           P  + MSPTTSNH+PGLASIL PQ+S   K A IG+D GR S  +H   N IS+ G++F 
Sbjct: 412 PGSKIMSPTTSNHLPGLASILQPQLSNTVKAATIGQDIGRSSHGDHIFPNKISSAGSNF- 470

Query: 429 QSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSM 488
            S+S  EPK   YRG +SSFG S SNGS VETL+ PQFLWGSP+  SE +   AW   S+
Sbjct: 471 NSHSLPEPKFSPYRGALSSFGASTSNGSSVETLTAPQFLWGSPNLSSEPTKPSAWPRPSV 530

Query: 489 GHPFS-SNGKIHGLPYSGRQGSFL----GSSQHHHVGSAPSGVPLERRFGFLPESPETSF 543
           GH  S SNG  H  PYS +  SF+        HHHVGSAPSG+P ER FGF P+S ETS 
Sbjct: 531 GHQLSTSNGTSHAFPYSSQNNSFVSSSQQQHHHHHVGSAPSGLPFERHFGFFPKSSETSL 590

Query: 544 MNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLG 602
           MN V + GMG+G NDG++M+N G   S N GI++PRN+ DNGSS FR+ SSP LSPVFLG
Sbjct: 591 MNNVGYRGMGLGHNDGNYMLNSG--ISGNVGISIPRNMPDNGSSNFRMRSSPILSPVFLG 648

Query: 603 NGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNI 662
           NGPYPGL P  +E   +R RSR I+ NNG+Q+D+KK FQL+L+KIRSGEDTRTTLMIKNI
Sbjct: 649 NGPYPGLLPTAMESFTDRVRSRWID-NNGSQVDNKKLFQLDLDKIRSGEDTRTTLMIKNI 707

Query: 663 PNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKK 722
           PNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP  IIPFYE F+GKK
Sbjct: 708 PNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIPFYETFHGKK 767

Query: 723 WEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQL 782
           WEKFNSEKVASLAYARIQG+ ALV HFQNSSLMNEDKRCRPI+FHS+G E  DQ+ QE L
Sbjct: 768 WEKFNSEKVASLAYARIQGKNALVNHFQNSSLMNEDKRCRPIVFHSDGSEVADQIVQEHL 827

Query: 783 --NSNSVNFQVCPSNGSHLRDASG 804
             NSN++  Q   S+   L D+ G
Sbjct: 828 PSNSNNMYIQAVKSSELQLSDSFG 851

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740630|emb|CBI30812.3| unnamed protein product [Vitis vinifera]

 Score = 1093 bits (2828), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 561/811 (69%), Positives = 623/811 (76%), Gaps = 98/811 (12%)

Query: 9   SLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDE 68
           SLPVLPHEKLNLN      QS+DD  +GL K+   V + + LE     AIG+ LPDDEDE
Sbjct: 74  SLPVLPHEKLNLNDTEHCCQSIDD--AGLDKLQQDVEAGESLEDDGIHAIGSLLPDDEDE 131

Query: 69  LLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNG 128
           LLAGIMDDFDL GL + +ED+E+YD+FGSGGGMELE +PQESL+M M+K+S+SD   GNG
Sbjct: 132 LLAGIMDDFDLSGLSNPMEDVEEYDLFGSGGGMELEIDPQESLNMGMAKVSLSDGVVGNG 191

Query: 129 LLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 188
           L  Y +PNG+GTVAGEHPYGEHPSRTLFVRNINSNVEDSELR LFEQYG IRTLYTACKH
Sbjct: 192 LAQYGLPNGSGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRTLFEQYGAIRTLYTACKH 251

Query: 189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 248
           RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPS
Sbjct: 252 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDVNQGTLVVFNLDPS 311

Query: 249 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           VSN+DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAAL+SLNRSDIAGKRIKLEP
Sbjct: 312 VSNDDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALRSLNRSDIAGKRIKLEP 371

Query: 309 SRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKS 368
           SRPGGARRNLMLQLNQELEQDESR  +H VGSP+ NSPPG+W QFSSPIEH+PLQ++SKS
Sbjct: 372 SRPGGARRNLMLQLNQELEQDESRSFRHHVGSPMANSPPGSWAQFSSPIEHSPLQSLSKS 431

Query: 369 PNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQ 428
           P FR +SPTTSNH+PGLASIL+ Q+S   K+APIGKDQGR                    
Sbjct: 432 PGFRTVSPTTSNHLPGLASILNSQISNSVKVAPIGKDQGR-------------------- 471

Query: 429 QSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSM 488
                            + FGP                    P+ YSEH++S AWQ  SM
Sbjct: 472 -----------------AKFGP-----------------ISCPAPYSEHTNSSAWQPPSM 497

Query: 489 GHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVA 548
           GHPF+SNG+  G PYSGR                      ER FG+ PESPE SFM PVA
Sbjct: 498 GHPFASNGQGRGFPYSGRH---------------------ERHFGYFPESPEASFMTPVA 536

Query: 549 FCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYP 607
           F GMG+  NDG+                   N+S++GS+ FR++SSPRLSP+F GNGP+P
Sbjct: 537 FGGMGLAHNDGT-------------------NMSESGSANFRMISSPRLSPMFPGNGPFP 577

Query: 608 GLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYT 667
           GL P+NIEGL +RGRSR +E NNGNQ+DSKKQFQL+L+KI +GEDTRTTLMIKNIPNKYT
Sbjct: 578 GLAPSNIEGLADRGRSRWVE-NNGNQIDSKKQFQLDLDKILNGEDTRTTLMIKNIPNKYT 636

Query: 668 SKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN 727
           SKMLLAAIDE H+GTYDFLYLPIDFKNKCNVGYAFINMLSP HIIPFY+AFNGKKWEKFN
Sbjct: 637 SKMLLAAIDEYHRGTYDFLYLPIDFKNKCNVGYAFINMLSPSHIIPFYQAFNGKKWEKFN 696

Query: 728 SEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSV 787
           SEKVASLAYARIQG+AALV HFQNSSLMNEDKRCRPILFHSEGPEAGDQ+ QE L SNS+
Sbjct: 697 SEKVASLAYARIQGKAALVTHFQNSSLMNEDKRCRPILFHSEGPEAGDQIIQEHLPSNSL 756

Query: 788 NFQVCPSNGSHLRDASGSPIADDEGNKPENS 818
           N QV   NGS + D   SP       KPE S
Sbjct: 757 NIQVPQPNGSQIGDTPESPEMVLLCEKPEKS 787

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450611|ref|XP_003595582.1| Polyadenylate-binding protein [Medicago truncatula] gi|355484630|gb|AES65833.1| Polyadenylate-binding protein [Medicago truncatula]

 Score = 1078 bits (2787), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 551/753 (73%), Positives = 620/753 (82%), Gaps = 14/753 (1%)

Query: 62  LPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISIS 121
           LPDD++ELLAGIMDDFDLRGLP SLEDLE+YD+F S GG+ELE +PQESLS+ +SK+S+S
Sbjct: 2   LPDDDEELLAGIMDDFDLRGLPGSLEDLEEYDLFDSSGGLELETDPQESLSVGISKLSLS 61

Query: 122 DSASGNGLLHYSVPNGAGTVAG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI 179
           DS+ GN +  YS+PNG G  A   EHPYGEHPSRTLFVRNINSNVED+ELR LFEQYGDI
Sbjct: 62  DSSVGNSMPPYSLPNGVGGGAVAGEHPYGEHPSRTLFVRNINSNVEDTELRTLFEQYGDI 121

Query: 180 RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 239
           RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGT
Sbjct: 122 RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGT 181

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE+YDVRAAEAALKSLNRSDI
Sbjct: 182 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEYYDVRAAEAALKSLNRSDI 241

Query: 300 AGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEH 359
           AGKRIKLEPSRPGGARRNLMLQLNQEL+QDESR  ++QVGSP+  SPPGNW+QF+SPIE 
Sbjct: 242 AGKRIKLEPSRPGGARRNLMLQLNQELDQDESRSFRYQVGSPLAGSPPGNWLQFNSPIEQ 301

Query: 360 NPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNT 419
           + L  ++ SP  + MSPTTSNH+PGLASIL PQ+S   K A IG+D GR S  +H   N 
Sbjct: 302 SSLPNLNHSPGSKIMSPTTSNHLPGLASILQPQLSNTVKAATIGQDIGRSSHGDHIFPNK 361

Query: 420 ISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSS 479
           IS+ G++F  S+S  EPK   YRG +SSFG S SNGS VETL+ PQFLWGSP+  SE + 
Sbjct: 362 ISSAGSNF-NSHSLPEPKFSPYRGALSSFGASTSNGSSVETLTAPQFLWGSPNLSSEPTK 420

Query: 480 SPAWQTSSMGHPFS-SNGKIHGLPYSGRQGSFL----GSSQHHHVGSAPSGVPLERRFGF 534
             AW   S+GH  S SNG  H  PYS +  SF+        HHHVGSAPSG+P ER FGF
Sbjct: 421 PSAWPRPSVGHQLSTSNGTSHAFPYSSQNNSFVSSSQQQHHHHHVGSAPSGLPFERHFGF 480

Query: 535 LPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSS 593
            P+S ETS MN V + GMG+G NDG++M+N G   S N GI++PRN+ DNGSS FR+ SS
Sbjct: 481 FPKSSETSLMNNVGYRGMGLGHNDGNYMLNSG--ISGNVGISIPRNMPDNGSSNFRMRSS 538

Query: 594 PRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDT 653
           P LSPVFLGNGPYPGL P  +E   +R RSR I+ NNG+Q+D+KK FQL+L+KIRSGEDT
Sbjct: 539 PILSPVFLGNGPYPGLLPTAMESFTDRVRSRWID-NNGSQVDNKKLFQLDLDKIRSGEDT 597

Query: 654 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 713
           RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP  IIP
Sbjct: 598 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIP 657

Query: 714 FYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEA 773
           FYE F+GKKWEKFNSEKVASLAYARIQG+ ALV HFQNSSLMNEDKRCRPI+FHS+G E 
Sbjct: 658 FYETFHGKKWEKFNSEKVASLAYARIQGKNALVNHFQNSSLMNEDKRCRPIVFHSDGSEV 717

Query: 774 GDQVTQEQL--NSNSVNFQVCPSNGSHLRDASG 804
            DQ+ QE L  NSN++  Q   S+   L D+ G
Sbjct: 718 ADQIVQEHLPSNSNNMYIQAVKSSELQLSDSFG 750

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567420|ref|XP_003551918.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1068 bits (2762), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 551/798 (69%), Positives = 630/798 (78%), Gaps = 10/798 (1%)

Query: 11  PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELL 70
           PVLPHEKL+L       Q VDD    L KVH      DP +     AIGN LPDDE++LL
Sbjct: 57  PVLPHEKLDLTDSENYGQPVDDNLLTLDKVHKEDEGHDPFDDFETNAIGNMLPDDEEDLL 116

Query: 71  AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLL 130
           AGIMDDFDL  LPS LEDL++ D+F +GGG E++ EPQESL++SMSKI ISD  + NG+ 
Sbjct: 117 AGIMDDFDLSKLPSQLEDLDENDLFVNGGGFEMDFEPQESLNISMSKIGISDGIASNGIG 176

Query: 131 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 190
            Y++PNG GTVAGEHPYGEHPSRTLFVRNINSNVEDSELR LFEQYGDIRTLYTACKHRG
Sbjct: 177 QYAIPNGVGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRTLFEQYGDIRTLYTACKHRG 236

Query: 191 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVS 250
           FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPSVS
Sbjct: 237 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDPSVS 296

Query: 251 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 310
           N+DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK+LNRSDIAGKRIKLEPSR
Sbjct: 297 NDDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKALNRSDIAGKRIKLEPSR 356

Query: 311 PGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPN 370
           PGGARRNLM QL+QELEQDE+R  +HQV SP+ NSPPG+W QF SP+E NPL + SKSP 
Sbjct: 357 PGGARRNLMQQLSQELEQDEARTFRHQVVSPVANSPPGSWAQFGSPVEQNPLASFSKSPG 416

Query: 371 FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQS 430
               SP  +NH+ GLA+IL PQ +T  KIAPIGKD GR +      +N+ S  GA+FQ S
Sbjct: 417 LGPASPINTNHLSGLAAILSPQATTSTKIAPIGKDPGRAA--NQMFSNSGSTQGAAFQHS 474

Query: 431 NSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGH 490
            SF E  +      +S+FG S S+ S + TLSGPQFLWGSP+ YSEHS++ AW +SS+G 
Sbjct: 475 ISFPEQNVKASPRPISTFGESSSSASSIGTLSGPQFLWGSPTPYSEHSNTSAWSSSSVGL 534

Query: 491 PFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFC 550
           PF+S+ +  G PY+     FLGS  HHHVGSAPSG+PL+R F + PESPE S M+PVAF 
Sbjct: 535 PFTSSVQRQGFPYTSNHSPFLGSHSHHHVGSAPSGLPLDRHFSYFPESPEASLMSPVAFG 594

Query: 551 GMGIGQNDGSFMV-NMGSRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPYPG 608
            +  G  DG+FM+ N+ +RASV  G+ +  N  +  S +FR+MS PR   +F GN  Y G
Sbjct: 595 NLNHG--DGNFMMNNISARASVGAGVGLSGNTPEISSPNFRMMSLPRHGSLFHGNSLYSG 652

Query: 609 LTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTS 668
               NIEGL ERGRSRR E N GNQ+DSKK +QL+L+KI  GEDTRTTLMIKNIPNKYTS
Sbjct: 653 PGATNIEGLAERGRSRRPE-NGGNQIDSKKLYQLDLDKIVCGEDTRTTLMIKNIPNKYTS 711

Query: 669 KMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNS 728
           KMLLAAIDENH+GTYDFLYLPIDFKNKCNVGYAFINM+SP HII FY+AFNGKKWEKFNS
Sbjct: 712 KMLLAAIDENHQGTYDFLYLPIDFKNKCNVGYAFINMVSPSHIIAFYKAFNGKKWEKFNS 771

Query: 729 EKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVN 788
           EKVASLAYARIQG+AALV HFQNSSLMNEDKRCRPILFHSEG + GD   QE   S+++N
Sbjct: 772 EKVASLAYARIQGKAALVMHFQNSSLMNEDKRCRPILFHSEGQDTGD---QEHFLSSNLN 828

Query: 789 FQVCPSNGSHLRDASGSP 806
             +   +GS+  D   SP
Sbjct: 829 ICIRQPDGSYSSDLLESP 846

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586946|ref|XP_002534073.1| RNA-binding protein, putative [Ricinus communis] gi|223525900|gb|EEF28317.1| RNA-binding protein, putative [Ricinus communis]

 Score = 1066 bits (2757), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 540/763 (70%), Positives = 619/763 (81%), Gaps = 14/763 (1%)

Query: 18  LNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDF 77
           L +N      QS+DD S  L+ V       DP E V   AIGN LPDDE+ELLAGIMDDF
Sbjct: 21  LKVNDSAHCGQSLDDGSPKLNNVELEFEDKDPFEDVEPNAIGNLLPDDEEELLAGIMDDF 80

Query: 78  DLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNG 137
           DL GLPS +EDLE+YD+FGSGGGMEL+ EPQESL + MSK++IS+  + NG+ HY++ NG
Sbjct: 81  DLSGLPSQVEDLEEYDLFGSGGGMELDFEPQESLRIGMSKLNISEGIAANGMSHYAISNG 140

Query: 138 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY 197
           A TVAGEHPYGEHPSRTLFVRNINSNVEDSEL++LFEQYGDIRTLYTACKHRGFVMISYY
Sbjct: 141 AATVAGEHPYGEHPSRTLFVRNINSNVEDSELKSLFEQYGDIRTLYTACKHRGFVMISYY 200

Query: 198 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQI 257
           DIR AR AMR LQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD SVSN+DLRQI
Sbjct: 201 DIRDARAAMRGLQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDASVSNDDLRQI 260

Query: 258 FGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           FGAYGEVKEIRETPHKRHHKFIEFYDVR+AEAAL++LNRSDIAGKRIKLEPSRPGGARRN
Sbjct: 261 FGAYGEVKEIRETPHKRHHKFIEFYDVRSAEAALRALNRSDIAGKRIKLEPSRPGGARRN 320

Query: 318 LMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPT 377
           LM QL+QELE DE+R  +HQVGSP+ NSPPGNW Q+ SP+EHNPL   + SP    +SP 
Sbjct: 321 LMQQLSQELENDEARSFRHQVGSPVANSPPGNWTQYGSPVEHNPLHGFNNSPGLGTLSPV 380

Query: 378 TSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPK 437
           +SN++PGLASIL   +S   KIAPIGKDQGR +     LTN    NG +FQ  +     K
Sbjct: 381 SSNNLPGLASILPSHISNPAKIAPIGKDQGRAN-TNQMLTN----NGVAFQHYDQ----K 431

Query: 438 IGLYRGTVSSFGP--SPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSN 495
                 ++S+FG   S SN SG+ TLSGPQFLWGSP+ YSE+ SS AW TSS+GH F S+
Sbjct: 432 PSTSPVSISAFGESNSNSNSSGIGTLSGPQFLWGSPTPYSENVSSSAWPTSSIGHAFVSS 491

Query: 496 GKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIG 555
            K  GLP++ R  SFLGS  HHHVGSAPSG+PL+R FGF PESPETS M P AF GMG+ 
Sbjct: 492 AKGQGLPHTSRHNSFLGSHYHHHVGSAPSGLPLDRHFGFFPESPETSLMTPNAFGGMGLN 551

Query: 556 QNDGSFMV-NMGSRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPYPGLTPAN 613
            N+G++++ N+G+RASV  GI +P +++++ S SFR+      SP+FLGN  Y G    +
Sbjct: 552 HNNGNYILNNIGARASVAAGIGLPGSITESSSPSFRMSFPSHNSPMFLGNASYLGPGTIS 611

Query: 614 IEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLA 673
            +   ERGRSRR+E N GNQ+DSKKQ+QL+L+KI SGED+RTTLMIKNIPNKYTSKMLLA
Sbjct: 612 SDVFAERGRSRRLE-NYGNQIDSKKQYQLDLDKIISGEDSRTTLMIKNIPNKYTSKMLLA 670

Query: 674 AIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVAS 733
           AIDENH+G YDFLYLPIDFKNKCNVGYAFINM SP HIIPFYEAFNGKKWEKFNSEKVAS
Sbjct: 671 AIDENHRGAYDFLYLPIDFKNKCNVGYAFINMASPSHIIPFYEAFNGKKWEKFNSEKVAS 730

Query: 734 LAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQ 776
           LAYARIQG+AALV+HFQNSSLMNEDKRCRPILFHSEG EAG+Q
Sbjct: 731 LAYARIQGKAALVSHFQNSSLMNEDKRCRPILFHSEGQEAGEQ 773

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	818
TAIR|locus:2013583	800	ML5 "MEI2-like protein 5" [Ara	0.737	0.753	0.537	2.4e-163
TAIR|locus:2156166	915	ML1 "MEI2-like protein 1" [Ara	0.314	0.280	0.566	1.3e-139
TAIR|locus:2182885	907	ML4 "MEI2-like 4" [Arabidopsis	0.315	0.284	0.566	9.3e-131
TAIR|locus:2117706	759	ML3 "MEI2-like 3" [Arabidopsis	0.734	0.791	0.460	4.2e-127
TAIR|locus:2045605	843	ML2 "MEI2-like 2" [Arabidopsis	0.694	0.673	0.450	4.1e-120
TAIR|locus:2090350	615	TEL1 "terminal EAR1-like 1" [A	0.113	0.151	0.526	5.7e-53
TAIR|locus:2008530	527	TEL2 "terminal EAR1-like 2" [A	0.140	0.218	0.446	6.7e-45
POMBASE|SPAC27D7.03c	750	mei2 "RNA-binding protein invo	0.162	0.177	0.548	5.2e-39
DICTYBASE|DDB_G0279255	1698	DDB_G0279255 [Dictyostelium di	0.124	0.060	0.470	3.6e-34
GENEDB_PFALCIPARUM|PFF1125c	427	PFF1125c "RNA-binding protein	0.139	0.266	0.495	3.5e-25

TAIR|locus:2013583 ML5 "MEI2-like protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 1590 (564.8 bits), Expect = 2.4e-163, P = 2.4e-163
 Identities = 346/644 (53%), Positives = 423/644 (65%)

Query:     8 SSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDED 67
             SSLPV P  KL L+    G   +DD  + +S+ +    S D  E   + +IGN LPD+ED
Sbjct:    33 SSLPVFPRGKLQLSDNRDGFSLIDD--TAVSRTNKFNESADDFE---SHSIGNLLPDEED 87

Query:    68 ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXXGN 127
              LL G+MDD DL  LP    D +DYD+FGSGGGMEL+ + ++                GN
Sbjct:    88 -LLTGMMDDLDLGELP----DADDYDLFGSGGGMELDADFRDNLSMSGPPRLSLSSLGGN 142

Query:   128 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 187
              +  +++PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSEL ALFEQYGDIRTLYT CK
Sbjct:   143 AIPQFNIPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELTALFEQYGDIRTLYTTCK 202

Query:   188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 247
             HRGFVMISYYDIR+AR AMR+LQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDP
Sbjct:   203 HRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKDNPSEKDMNQGTLVVFNLDP 262

Query:   248 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
             S+SN+DL  IFGA+GE+KEIRETPHKRHHKF+EFYDVR AEAALK+LNR +IAGKRIK+E
Sbjct:   263 SISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKVE 322

Query:   308 PSRPGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPP--GNWVQFSSPIEHNPLQTI 365
             PSRPGGARR+LM              L   +GSP+ NSPP  GNW   +SP+E +PLQ++
Sbjct:   323 PSRPGGARRSLMLQLNQDLENDDLHYLP-MIGSPMANSPPMQGNW-PLNSPVEGSPLQSV 380

Query:   366 -SKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANG 424
              S+SP F  +SPT + H+ GLAS L+ Q  +  K+APIG+ Q             I +NG
Sbjct:   381 LSRSPVF-GLSPTRNGHLSGLASALNSQGPS-SKLAPIGRGQ-------------IGSNG 425

Query:   425 ASFQQSNS-FSEPKI-GLYRGTVXXXXXXXXXXXXVETLSGPQFLWGXXXXXXXXXXXPA 482
               FQQS+  F EPK+   Y G +            +ETLSG +FLWG             
Sbjct:   426 --FQQSSHLFQEPKMDNKYTGNLSPSGPLISNGGGIETLSGSEFLWGSPNARSEPSSSSV 483

Query:   483 WQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETS 542
             W TSS G+P  S      +P+  +  +   S  H HVGSAPSGVPLE+ FGF+PES + +
Sbjct:   484 WSTSSTGNPLFSTRVDRSVPFPHQHQNQSRSHHHFHVGSAPSGVPLEKHFGFVPESSKDA 543

Query:   543 -FMNPVAFCGM-GIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVF 600
              FMN V   GM G+G N GSF   M +   +N G ++  N     SS+R+MSSPR SP+F
Sbjct:   544 LFMNTVGLQGMSGMGLNGGSFSSKMANNGIINSG-SMAEN---GFSSYRMMSSPRFSPMF 599

Query:   601 LGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKK-QFQLE 643
             L +G  PG   +  + LYE GR RR+ENN+      K+ Q  LE
Sbjct:   600 LSSGLNPGRFASGFDSLYENGRPRRVENNSNQVESRKQFQLDLE 643

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2156166 ML1 "MEI2-like protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 722 (259.2 bits), Expect = 1.3e-139, Sum P(4) = 1.3e-139
 Identities = 153/270 (56%), Positives = 193/270 (71%)

Query:   513 SSQHHHVGSAPS-GVPL-ERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRAS 570
             S  HHH+GSAP    P  +RR  ++ ES E+S  +  +   MGI  +  S  +++GS  +
Sbjct:   603 SPVHHHIGSAPVLNSPFWDRRQAYVAESLESSGFHIGSHGSMGIPGSSPSHPMDIGSHKT 662

Query:   571 VNPGITVPRNLSDNGSSFRVMSSPR-LSPVFLGNGPYPGLTPANIEGLYERGRS---RRI 626
              + G     N  D  S   V+ SP+ LS +F G  P  G  P + +   ER R+   RR 
Sbjct:   663 FSVG----GNRMDVNSQNAVLRSPQQLSHLFPGRSPM-GSMPGSFDSPNERYRNLSHRRS 717

Query:   627 ENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL 686
             E+++ N    KK ++L++++I  GED RTTLMIKNIPNKYTSKMLL+AIDE+ KGTYDFL
Sbjct:   718 ESSSSNA--DKKLYELDVDRILRGEDRRTTLMIKNIPNKYTSKMLLSAIDEHCKGTYDFL 775

Query:   687 YLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 746
             YLPIDFKNKCNVGYAFIN++ P  I+PF++AFNGKKWEKFNSEKVA+L YARIQG+ AL+
Sbjct:   776 YLPIDFKNKCNVGYAFINLIEPEKIVPFFKAFNGKKWEKFNSEKVATLTYARIQGKTALI 835

Query:   747 AHFQNSSLMNEDKRCRPILFHSEGPEAGDQ 776
             AHFQNSSLMNEDKRCRPILFH++GP AGDQ
Sbjct:   836 AHFQNSSLMNEDKRCRPILFHTDGPNAGDQ 865

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0048507 "meristem development" evidence=IGI

GO:0045836 "positive regulation of meiosis" evidence=IGI

TAIR|locus:2182885 ML4 "MEI2-like 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 711 (255.3 bits), Expect = 9.3e-131, Sum P(3) = 9.3e-131
 Identities = 153/270 (56%), Positives = 190/270 (70%)

Query:   513 SSQHHHVGSAPS-GVPL-ERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRAS 570
             S  HHH+GSAP    P  +RR  ++ ESPE+S  +  +   MG   +  S  ++ GS   
Sbjct:   600 SPVHHHIGSAPVLNSPFWDRRQAYVAESPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKV 659

Query:   571 VNPGITVPRNLSDNGSSFRVMSSPRLSP-VFLGNGPYPGLTPANIEGLYERGRS---RRI 626
              +    V  N  +  S   V+ S R  P +F G  P   ++  + +   ER R+   RR 
Sbjct:   660 FSH---VGGNRMEANSKNAVLRSSRQMPHLFTGRSPMLSVS-GSFDLPNERYRNLSHRRS 715

Query:   627 ENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL 686
             E+N+ N    KK ++L++++I  GED+RTTLMIKNIPNKYTSKMLLAAIDE  KGTYDFL
Sbjct:   716 ESNSSNA--EKKLYELDVDRILRGEDSRTTLMIKNIPNKYTSKMLLAAIDEYCKGTYDFL 773

Query:   687 YLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 746
             YLPIDFKNKCNVGYAFIN++ P +I+PFY+AFNGKKWEKFNSEKVASLAY RIQG++AL+
Sbjct:   774 YLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAYGRIQGKSALI 833

Query:   747 AHFQNSSLMNEDKRCRPILFHSEGPEAGDQ 776
             AHFQNSSLMNEDKRCRPILFH+ GP AGDQ
Sbjct:   834 AHFQNSSLMNEDKRCRPILFHTAGPNAGDQ 863

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0048507 "meristem development" evidence=IGI

TAIR|locus:2117706 ML3 "MEI2-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 1248 (444.4 bits), Expect = 4.2e-127, P = 4.2e-127
 Identities = 297/645 (46%), Positives = 385/645 (59%)

Query:     8 SSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVAS--DDPLEGVMNPAIGNSLPDD 65
             SSLP++ H+  N+N      QSVD+++SGL     G+ +  DD   G  +P IGN LPDD
Sbjct:    25 SSLPLIQHQ--NINPRDSYHQSVDEMASGLDHFSGGIGNMLDD---GDSHP-IGNMLPDD 78

Query:    66 EDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXX 125
             E+EL +G+MDD +L  LP++L+DLEDYD+FGSGGG+ELE +P +                
Sbjct:    79 EEELFSGLMDDLNLSSLPATLDDLEDYDLFGSGGGLELETDPYDSLNKGFSRMGFADSNV 138

Query:   126 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA 185
              N +      NG G++AGEHPYGEHPSRTLFVRNINSNVEDSEL+ALFEQYG IRTLYTA
Sbjct:   139 DNVMPQNIFQNGVGSIAGEHPYGEHPSRTLFVRNINSNVEDSELQALFEQYGHIRTLYTA 198

Query:   186 CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNL 245
             CK RGFVM+SY DIRA+R AMRALQ K L++RKLDIHFSIPKDNPS+KD+NQGTLVVFNL
Sbjct:   199 CKQRGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNL 258

Query:   246 DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
              PSVSN DL  IFG YGE+KEIRETP+KRHHKF+EF+DVR+A+AALK+LNR++IAGKRIK
Sbjct:   259 APSVSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADAALKALNRTEIAGKRIK 318

Query:   306 LEPSRPGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTI 365
             LE SRPGGARRN+M           S    + V SP+ +SP GNW   +SPI+H PLQ+ 
Sbjct:   319 LEHSRPGGARRNMMLQMNPELEQDDSYSYLNHVESPLASSPIGNWR--NSPIDH-PLQSF 375

Query:   366 SKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQ-GRG-SLMEHALTNTISAN 423
             SKSP F N+SPT +        I +P+ S   K A +  DQ GR  S ++H  +++ S N
Sbjct:   376 SKSPIFGNLSPTKN--------IRYPEFSM--KTASVNNDQEGRRFSHLDHLFSSS-SYN 424

Query:   424 GASFQQSNSFSEPKIGLYRGTVXXXXXXXXXXXXVETLSGPQFLWGXXXXXXXXXXXPAW 483
              AS + S +F +P+     G+V            VETLSG +FLWG            + 
Sbjct:   425 NASHKAS-TFQQPQSF---GSVSSFGSLNSHPSHVETLSGSEFLWGSPSSSAWPVNPFSS 480

Query:   484 QTSSMGHPFSS-NGKIHGLPYSGR--QGSFLGSSQHHHVGS-----APSGVPLERRFGFL 535
                +   P+S+ NG +H L + G    G F  S +   +GS     A   +  +R    L
Sbjct:   481 NRENHRFPYSAQNGSLHQLHHIGSAPSGFFPRSPETSSMGSVAFRGASGNMNAQRN---L 537

Query:   536 PESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRN--LSDNGSS--FRVM 591
              E+   +F    A     +   +GS++    +  S++  +    N     NG+    ++ 
Sbjct:   538 RETSSPNFKMLSAPRRSQLFTGNGSYLWPAATMVSIDDPLEDGSNQQFDSNGNQADIKIQ 597

Query:   592 SSPRLSPVFLGNGPYPGLTPANIEGLYERGRS-RRIENNNGNQLD 635
                 LS +  G  P   L   NI   Y R      I+  N    D
Sbjct:   598 FQLDLSKIMRGEDPRTTLMIKNIPNKYTRNMLLAAIDEKNSGTYD 642

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

TAIR|locus:2045605 ML2 "MEI2-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1182 (421.1 bits), Expect = 4.1e-120, P = 4.1e-120
 Identities = 266/590 (45%), Positives = 345/590 (58%)

Query:     8 SSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDED 67
             SSLP L HEKLN+        S D+ S  L+K+  G +  D LE V   A+   LP+DE+
Sbjct:    54 SSLPTLFHEKLNMTDSD-SWLSFDESSPNLNKLVIGNSEKDSLEDVEPDALEILLPEDEN 112

Query:    68 ELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXXGN 127
             ELL G++D+ +  GLP  L+DLE+ D+F +GGGMEL+ E Q+                 N
Sbjct:   113 ELLPGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVESQDNHAVDASGMQISDRGAAN 172

Query:   128 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 187
               +    PN AG V+ EHP GEHPSRTLFVRNINS+VEDSEL ALFE +G+IR+LYTACK
Sbjct:   173 AFVPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVEDSELSALFEPFGEIRSLYTACK 232

Query:   188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 247
              RGFVMISYYDIRAA  AMRALQN  LR+R LDIHFSIPK+NPS+KD+NQGTLV+FN+D 
Sbjct:   233 SRGFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDT 292

Query:   248 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
             +VSN++L Q+FGAYGE++EIRETP++R H+FIE+YDVR AE ALK+LNRS+I GK IKLE
Sbjct:   293 TVSNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLE 352

Query:   308 PSRPGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISK 367
              SRPGGARR  +                +QVGS + NSPPGNW    SP++ +P    ++
Sbjct:   353 LSRPGGARRLSVPSQSQDLERTEVTNFYNQVGSHVANSPPGNW-PIGSPVKGSPSHAFTR 411

Query:   368 SPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASF 427
                   + P  S++MPGLASIL    S+    +P+  DQG  +     + N    +  S+
Sbjct:   412 PHGLGMVRPVNSDNMPGLASILPAHPSSFHGFSPVSNDQGLLNHSNQTILNKGLMHNISY 471

Query:   428 QQSNSFSEPKIGLYRGTVXXXXXXXXXXXXVETLSGPQFLWGX--XXXXXXXXXXPAWQT 485
              Q +S  E   G   G                T S  ++ WG              +  +
Sbjct:   472 GQPHSLPEHITG---GISNSMRFIAPHSSGFGTSSDHRYRWGSPPQHMNYPGYTGVSSSS 528

Query:   486 SSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMN 545
             SS   PF+     HG P++ RQ S LG  QHH VGSAPS +    +      SPE     
Sbjct:   529 SSTERPFTVR---HGFPFAERQASLLGKYQHH-VGSAPSSIHFNTQMNCYTGSPEI---- 580

Query:   546 PVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNG-SSFRVMSSP 594
             P+ F  MGI +N  S      +    N G+++P N S+   + F + S P
Sbjct:   581 PLGFSDMGINRNYNS------AHGKANLGVSLPGNSSEQDFTGFGMSSMP 624

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

TAIR|locus:2090350 TEL1 "terminal EAR1-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 5.7e-53, Sum P(4) = 5.7e-53
 Identities = 49/93 (52%), Positives = 65/93 (69%)

Query:   223 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY 282
             F +P  +      NQGTLV+FNLDP VS+  LRQIF  YG +KE+RETP+K+H +F+EFY
Sbjct:   198 FVVPATSAVPGGCNQGTLVIFNLDPEVSSITLRQIFQVYGPIKELRETPYKKHQRFVEFY 257

Query:   283 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 315
             DVR A  A   +N  +I GK++ +E SRPGG +
Sbjct:   258 DVRDAARAFDRMNGKEIGGKQVVIEFSRPGGIK 290

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

TAIR|locus:2008530 TEL2 "terminal EAR1-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 6.7e-45, Sum P(3) = 6.7e-45
 Identities = 59/132 (44%), Positives = 78/132 (59%)

Query:   652 DTRTTLMIKNIPNKYTSKMLLAAID------------ENHK---GTYDFLYLPIDFKNKC 696
             D RTT+MIKNIPNKYT K+LL  +D            E +K    +YDF+YLPIDF NK 
Sbjct:   334 DGRTTVMIKNIPNKYTQKLLLKMLDTHCKDCNQSVIKEGNKTPMSSYDFVYLPIDFSNKS 393

Query:   697 NVGYAFINMLSPLHIIPFYEAFNGKKWEKFNS-EKVASLAYARIQGRAALVAHFQNSSLM 755
             NVGY F+NM SP  +   Y++F+ + W  F +  K+  + YARIQG  +L  HF+N  L 
Sbjct:   394 NVGYGFVNMTSPEAVWRLYKSFHNQHWRDFTTTRKICEVTYARIQGLESLREHFKNVRLA 453

Query:   756 N-EDKRCRPILF 766
               E     P++F
Sbjct:   454 GVEIDEYMPVVF 465

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

POMBASE|SPAC27D7.03c mei2 "RNA-binding protein involved in meiosis Mei2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 375 (137.1 bits), Expect = 5.2e-39, Sum P(3) = 5.2e-39
 Identities = 73/133 (54%), Positives = 94/133 (70%)

Query:   642 LELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYA 701
             ++  +I SG DTRTT+MIKNIPNK+T +ML   ID  +KGTYDFLYL IDF NKCNVGYA
Sbjct:   584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query:   702 FINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRC 761
             FIN + P  II F +A  G +W  F+SEK+  ++YA IQG+  L+  F+NS +M+E+   
Sbjct:   644 FINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQGKDRLIEKFRNSCVMDENPAY 703

Query:   762 RPILFHSEGPEAG 774
             RP +F S GP  G
Sbjct:   704 RPKIFVSHGPNRG 716

GO:0003723 "RNA binding" evidence=IDA

GO:0004860 "protein kinase inhibitor activity" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007127 "meiosis I" evidence=TAS

GO:0033620 "Mei2 nuclear dot" evidence=IDA

GO:0034064 "Tor2-Mei2-Ste11 complex" evidence=IDA

GO:0045836 "positive regulation of meiosis" evidence=IMP

DICTYBASE|DDB_G0279255 DDB_G0279255 [Dictyostelium discoideum (taxid:44689)]

 Score = 248 (92.4 bits), Expect = 3.6e-34, Sum P(3) = 3.6e-34
 Identities = 48/102 (47%), Positives = 67/102 (65%)

Query:   645 EKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFIN 704
             E I SG DTRT+LMI+NIPN+ T + L A IDE  K TYDFL +P+D   K + GYAFIN
Sbjct:  1564 ENIISGVDTRTSLMIRNIPNRLTQQTLTALIDEEFKDTYDFLNMPLDPHTKVSRGYAFIN 1623

Query:   705 MLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 746
                 +++  F++ F   +W+ +N +K+  + YA IQG  AL+
Sbjct:  1624 FKDHMNVYRFHQKFFHTRWKNYNHDKICEINYAIIQGEEALL 1665

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GENEDB_PFALCIPARUM|PFF1125c PFF1125c "RNA-binding protein mei2 homologue, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 306 (112.8 bits), Expect = 3.5e-25, P = 3.5e-25
 Identities = 57/115 (49%), Positives = 79/115 (68%)

Query:   655 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPF 714
             TT+M++NIPNKYT  ML+  ++E+ KG YDF YLPIDF+NKCNVGYAFIN + P +   F
Sbjct:   290 TTVMLRNIPNKYTQNMLMDVMNEHFKGLYDFFYLPIDFRNKCNVGYAFINFIHPYYAELF 349

Query:   715 YEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNED-KRCRPILFHS 768
              + FN  K   F S KV S+ + R+QG  A + H++NS++M     + +PILF +
Sbjct:   350 IKFFNNYKLNAFKSNKVCSVTWGRVQGLKANIEHYRNSAIMTIPIPQYKPILFQN 404

GO:0003723 "RNA binding" evidence=ISS

GO:0045836 "positive regulation of meiosis" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8VWF5	AML5_ARATH	No assigned EC number	0.6288	0.9022	0.9225	yes	no
Q6ZI17	OML2_ORYSJ	No assigned EC number	0.6004	0.9474	0.9139	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	818
pfam04059	97	pfam04059, RRM_2, RNA recognition motif 2	6e-65
cd12531	86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	9e-63
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-49
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	8e-44
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	4e-43
cd12530	101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	6e-38
cd12532	90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	8e-37
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	8e-32
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-31
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	1e-28
smart00360	73	smart00360, RRM, RNA recognition motif	8e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-14
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-12
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	4e-12
smart00360	73	smart00360, RRM, RNA recognition motif	5e-12
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	6e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-11
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-10
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	7e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-09
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	8e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-08
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-08
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-08
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	7e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-07
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-07
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	6e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	8e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	8e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	4e-06
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-06
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	5e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-06
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	6e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	8e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	1e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	1e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	3e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-05
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	5e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	5e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-05
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	6e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	7e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	8e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	8e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	9e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	9e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-04
cd12288	93	cd12288, RRM_La_like_plant, RNA recognition motif	1e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-04
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	2e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-04
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	3e-04
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	3e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	5e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-04
cd12697	76	cd12697, RRM3_ROD1, RNA recognition motif 3 in ver	5e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-04
cd12695	93	cd12695, RRM3_PTBP1, RNA recognition motif 3 in ve	6e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	6e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	6e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	7e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	7e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	7e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	7e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	7e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	7e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	8e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	8e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	8e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	9e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.001
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.001
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
cd12256	89	cd12256, RRM2_LKAP, RNA recognition motif 2 in Lim	0.001
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.001
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.001
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.001
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.001
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.001
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.001
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.001
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.001
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12419	80	cd12419, RRM_Ssp2_like, RNA recognition motif in y	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.002
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	0.002
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.003
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.003
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	0.003
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.003
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.003
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	0.003
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.004
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.004
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.004
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.004
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.004
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.004
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.004
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.004
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.004
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.004
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.004
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.004
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.004

>gnl|CDD|112856 pfam04059, RRM_2, RNA recognition motif 2

 Score =  211 bits (538), Expect = 6e-65
 Identities = 85/97 (87%), Positives = 90/97 (92%)

Query: 654 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 713
           RTTLMIKNIPNKYT KMLLAAIDE +KGTYDFLYLPIDFKNKCNVGYAFINM+ P  IIP
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIP 60

Query: 714 FYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQ 750
           F +AFNGKKWEKFNSEKVASLAYARIQG+ AL+AHFQ
Sbjct: 61  FGKAFNGKKWEKFNSEKVASLAYARIQGKDALIAHFQ 97

Length = 97

>gnl|CDD|240975 cd12531, RRM3_MEI2_like, RNA recognition motif 3 in plant Mei2-like proteins

 Score =  204 bits (522), Expect = 9e-63
 Identities = 75/86 (87%), Positives = 80/86 (93%)

Query: 657 LMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYE 716
           LMIKNIPNKYT KMLLAAIDE H+GTYDF YLPIDFKNKCNVGYAFINM+SP  I+PFY+
Sbjct: 1   LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYK 60

Query: 717 AFNGKKWEKFNSEKVASLAYARIQGR 742
           AFNGKKWEKFNSEKV SLAYARIQG+
Sbjct: 61  AFNGKKWEKFNSEKVCSLAYARIQGK 86

This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 86

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score =  168 bits (428), Expect = 1e-49
 Identities = 66/77 (85%), Positives = 69/77 (89%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           SRTLFVRNINSNVED ELRALFEQ+GDIRTLYTACKHRGF+M+SYYDIRAAR A RALQ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 212 KPLRRRKLDIHFSIPKD 228
             L  RKLDIHFSIPKD
Sbjct: 61  TELGGRKLDIHFSIPKD 77

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score =  151 bits (384), Expect = 8e-44
 Identities = 64/71 (90%), Positives = 70/71 (98%)

Query: 237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           QGTLVVFNLDPSVSN+DL QIFGAYGE+KEIRETP+KRHHKFIEFYDVR+AEAALK+LNR
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 297 SDIAGKRIKLE 307
           S+IAGKRIKLE
Sbjct: 61  SEIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  150 bits (381), Expect = 4e-43
 Identities = 58/86 (67%), Positives = 70/86 (81%), Gaps = 1/86 (1%)

Query: 657 LMIKNIPNKYTSKMLLAAIDENHKG-TYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFY 715
           +MI+NIPNKYT +MLL  +DE+ KG  YDFLYLPIDFKNKCNVGYAFIN ++P +   FY
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 716 EAFNGKKWEKFNSEKVASLAYARIQG 741
           +AFNGKKW+ F S+KV  + YARIQG
Sbjct: 61  KAFNGKKWKNFKSKKVCDITYARIQG 86

This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 86

>gnl|CDD|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal EAR1-like proteins

 Score =  136 bits (344), Expect = 6e-38
 Identities = 53/101 (52%), Positives = 70/101 (69%), Gaps = 13/101 (12%)

Query: 654 RTTLMIKNIPNKYTSKMLL-----------AAIDENH--KGTYDFLYLPIDFKNKCNVGY 700
           RTTLMIKNIPNKY+ K+LL             I+++     +YDF+YLPIDFKNKCN+GY
Sbjct: 1   RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHIEDSSQPVSSYDFVYLPIDFKNKCNLGY 60

Query: 701 AFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQG 741
           AF+N  SP     FY+AF+ ++WE+FNS K+  + YAR+QG
Sbjct: 61  AFVNFTSPEATWRFYKAFHNQQWEEFNSRKICQITYARVQG 101

This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 101

>gnl|CDD|240976 cd12532, RRM3_MEI2_fungi, RNA recognition motif 3 in fungal Mei2-like proteins

 Score =  133 bits (335), Expect = 8e-37
 Identities = 53/89 (59%), Positives = 67/89 (75%)

Query: 654 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 713
           RTT+M+KNIPNK+T +ML   IDE + GTYDF+YL IDF N CNVGYAF+N + P+ II 
Sbjct: 1   RTTVMLKNIPNKFTQQMLRKYIDETNPGTYDFMYLRIDFNNSCNVGYAFVNFIEPISIIT 60

Query: 714 FYEAFNGKKWEKFNSEKVASLAYARIQGR 742
           F +A  G KW  F+SEKV  ++YA IQG+
Sbjct: 61  FGKARVGTKWNMFHSEKVCDISYANIQGK 89

This subgroup corresponds to the RRM3 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 90

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  117 bits (296), Expect = 8e-32
 Identities = 40/71 (56%), Positives = 55/71 (77%)

Query: 237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           QGTL+VFNLD  +S+++LR +F  +GEVK+IRETP +   KF+EFYD+RAAEAAL +LN 
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 297 SDIAGKRIKLE 307
               G R+K++
Sbjct: 61  RPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score =  116 bits (292), Expect = 2e-31
 Identities = 42/71 (59%), Positives = 57/71 (80%)

Query: 237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           QGTLV+FNLDP+VS+E LR IF  YG+VKE+RETP KR  +F+EF+DVR A  AL+++N 
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 297 SDIAGKRIKLE 307
            +I+GK + +E
Sbjct: 61  KEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  108 bits (272), Expect = 1e-28
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           SR+LFV N+  +V +S LR LFE YGD+R + T     G V + +YDIR A+ A+R L  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 212 KPLRRRKLDIH 222
           + ++++ L   
Sbjct: 61  RHMQQQALGGS 71

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 72.2 bits (178), Expect = 8e-16
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
           TL V NL P  + E+LR++F  +G+V+ +R    K   K     F+EF     AE AL++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 294 LNRSDIAGKRIKL 306
           LN  ++ G+ +K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 71.6 bits (176), Expect = 1e-15
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN 295
           L V NL P  + EDLR++F  +GE++ +R    +    +   F+EF     AE AL++LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 296 RSDIAGKRIKLE 307
             ++ G+++K+ 
Sbjct: 61  GKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 66.5 bits (163), Expect = 8e-14
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN 295
           L V NL P  + EDL+ +F  +G ++ IR    ET   +   F+EF D   AE AL++LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 296 RSDIAGKRIK 305
             ++ G+ ++
Sbjct: 61  GKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 21/73 (28%), Positives = 44/73 (60%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           TL V N++ +V +E+LR +F  +G+++ +      R    + +YD+RAA  A ++L  ++
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 299 IAGKRIKLEPSRP 311
           + G+++ +  S P
Sbjct: 63  LGGRKLDIHFSIP 75

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 213
           TL V N++S + D ELR+LF Q+G+++ +           + +YDIRAA  A+ AL  +P
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62

Query: 214 LRRRKLDI 221
               +L +
Sbjct: 63  FLGGRLKV 70

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 61.8 bits (151), Expect = 5e-12
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA 208
           TLFV N+  +  + ELR LF ++G + ++         K +GF  + +     A  A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 209 LQNKPLRRRKLDI 221
           L  K L  R L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 61.4 bits (150), Expect = 6e-12
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 8/78 (10%)

Query: 154 TLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAM 206
           TL++ N+N  ++  EL+    ALF Q+G   DI    T  K RG   + + D+ +A  A+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL-KMRGQAFVVFKDVESATNAL 59

Query: 207 RALQNKPLRRRKLDIHFS 224
           RALQ  P   + + I ++
Sbjct: 60  RALQGFPFYDKPMRIQYA 77

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQ 210
           LFV N+  +  + +LR LF ++G+I ++        K +GF  + +     A  A+ AL 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 211 NKPLRRRKLDIH 222
            K L  RKL + 
Sbjct: 61  GKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V NL  +V+ EDL+ +FG +GEV        RET   R   F+E      A AA++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 294 LNRSDIAGKRIKLEPSRP 311
           LN +D  G+ + +  +RP
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 58.4 bits (142), Expect = 9e-11
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALK 292
             L V  L    + ++L  +F  +G V+E+      ET   R   F+ F  V  A+AA++
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 293 SLNRSDIAGKRIKLEPSR 310
            LN  ++ G+ IK+E ++
Sbjct: 62  DLNGKELEGRVIKVEKAK 79

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 57.7 bits (140), Expect = 1e-10
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE-AALKSLNRS 297
           TL V  L   V+ +DLR  F  +GE++ I   P ++   F+ F    AAE AA +  N+ 
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-RQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 298 DIAGKRIKL 306
            I G+R+KL
Sbjct: 62  IINGRRLKL 70

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 55.6 bits (135), Expect = 4e-10
 Identities = 14/56 (25%), Positives = 24/56 (42%)

Query: 169 LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 224
           L  LF  +G++  +    K  GF  + +    AA  A++ L       R L + +S
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 55.8 bits (135), Expect = 7e-10
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAARTAMRA 208
           +L+VRN+       +LR LF +YG I  +Y          RGF  + + D+R A  A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 209 LQNKPLRRRKLDIHFS 224
           L       R+++I F+
Sbjct: 62  LDRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 54.9 bits (133), Expect = 9e-10
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           V NL P  +  +L   F  YG ++ +   R  P      F+EF D R AE A+++L+   
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG---FAFVEFEDPRDAEDAVRALDGRR 60

Query: 299 IAGKRIKLEPSRP 311
           I G R+++E SR 
Sbjct: 61  ICGNRVRVELSRG 73

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNR 296
           L V NL PSV+ EDLR+ F  YG+V+ +R   +K   +   F+EF     AEAALK LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 297 SDIAGKRIK 305
             + G+ ++
Sbjct: 61  LVLDGRTLR 69

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQ 210
           LFV N+  +  + +L+ LF ++G I ++        + +GF  + + D   A  A+ AL 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 211 NKPLRRRKL 219
            K L  R+L
Sbjct: 61  GKELGGREL 69

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 54.5 bits (132), Expect = 2e-09
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HK---FIEFYDVRAAEAALKS 293
            L+V N+    + ++LR++F  +G+VK +R  P K    H+   F+EF   + A+ A+++
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 294 LNRSDIAGKRIKLEPS 309
           L  + + G+ + LE +
Sbjct: 61  LKSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 295
           ++ V  L P V+ E+L + F  +G++ E   I+   H     FI+F   +AA  A++S N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 296 RSDIAGKRIKLE 307
            S +  K + ++
Sbjct: 65  HSMLKNKTMHVQ 76

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.9 bits (128), Expect = 3e-09
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 254 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 309
           L ++F  +G V++I+    K    F+EF    AAE A++ LN     G+ ++++ S
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 53.1 bits (128), Expect = 5e-09
 Identities = 26/68 (38%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           T+ V  LDP+V+ ++LR +FG +GE+  ++  P  +   F++F    AAEAA++ L  + 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVK-IPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61

Query: 299 IAGKRIKL 306
           I G RI+L
Sbjct: 62  IGGSRIRL 69

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 52.8 bits (127), Expect = 8e-09
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
           +L V N+  +   +DLR++FG YG + ++       T   R   +++F DVR AE AL  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 294 LNRSDIAGKRIKLE 307
           L+R+   G+ I+++
Sbjct: 62  LDRTRFLGREIEIQ 75

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 58.3 bits (141), Expect = 1e-08
 Identities = 52/216 (24%), Positives = 92/216 (42%), Gaps = 35/216 (16%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAARTAMRAL 209
           L+V+N++ +V + +LR LF ++G+I +     K      RGF  +++     A  A+  +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 210 -------------------QNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSV 249
                              Q +  R  +L   F   +     K   QG  L V NLD +V
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFE--ELQQERKMKAQGVNLYVKNLDDTV 297

Query: 250 SNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
           ++E LR++F   GE+   +    E    R   F+ F +   A  A+  ++   + GK + 
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLY 357

Query: 306 LEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 341
           +  ++    RR     L  +  Q + R+ Q  +GSP
Sbjct: 358 VALAQRKEQRRA---HLQDQFMQLQPRMRQLPMGSP 390

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 17/59 (28%), Positives = 33/59 (55%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           SR L +  +  ++ +++LR   EQ+G +R +       G V + +YD+R A  A+R ++
Sbjct: 1   SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDAMAEGIVTVHFYDLRHAEDALRDIR 59

This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 57.2 bits (138), Expect = 2e-08
 Identities = 45/176 (25%), Positives = 87/176 (49%), Gaps = 19/176 (10%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 203
           E   RT+FV  +     + +L   F + G +R +       + + +G   + +YD+ +  
Sbjct: 86  ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVI 145

Query: 204 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN--QGT------LVVFNLDPSVSNEDLR 255
            A+ AL  + L  R + +  S  + N + K      G       L V NL  +++ ++LR
Sbjct: 146 KAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 256 QIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           QIF  +G++++++     ET   +   FI+F+D   A+ AL+ +N  ++AG+ IK+
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 260

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal Mei2-like proteins

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-RGFVMISYYDIRAARTAMRALQ 210
           +R L V  +  +V  S L+ +FE+ GD++ ++      +G V++S++D+R A  A + LQ
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 211 NKPL 214
           +K  
Sbjct: 61  SKRA 64

This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 72

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 57.1 bits (138), Expect = 3e-08
 Identities = 47/197 (23%), Positives = 94/197 (47%), Gaps = 15/197 (7%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQ 210
           +FV+N++ +V++  L   F ++G+I +   A     K RG+  + +    +A+ A++ + 
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 211 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 268
              L  +++ +   I K       L + T L V NLDPSV+ + LR++F  +GE+     
Sbjct: 151 GMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV 210

Query: 269 ---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI----AGKRIKLEPSRPGGARRNLMLQ 321
               +   R   F+ F     A  A++ +N   I     GK++ +  ++    R   + +
Sbjct: 211 MKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRR 270

Query: 322 LNQELEQDESRILQHQV 338
             +EL+Q+  R ++ Q 
Sbjct: 271 KFEELQQE--RKMKAQG 285

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 294
           L+V NL    +  DL+++F  +G V E+   P K   K     F++F     AE A+K +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEV-TIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 295 NRSDIAGKRI 304
           N   I G+ +
Sbjct: 61  NGKKIKGRPV 70

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 50.6 bits (122), Expect = 4e-08
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V  L  +V+ + L++IF  YG VK++     RE    R + ++EF     AE A+K +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 295 NRSDIAGKRIKLE 307
           +   I G+ + +E
Sbjct: 61  DGGQIDGQEVTVE 73

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRT----------LYTACKHRGFVMISYYDIRAA 202
            TLFV+N+N    +  L+  FE+ G +R+                  G+  + +    AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 203 RTAMRALQNKPLRRRKLDIHFS 224
           + A++ LQ   L    L++  S
Sbjct: 61  QKALKRLQGTVLDGHALELKLS 82

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 9/75 (12%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHK---FIEFYDVRAAEAALKS 293
           V NLD  +  +DLR IF  +GEV+ IR     +    R +    F+ F D  +AE AL+ 
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ- 63

Query: 294 LNRSDIAGKRIKLEP 308
           LN +++ G++I +  
Sbjct: 64  LNGTELGGRKISVSL 78

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 50.4 bits (121), Expect = 7e-08
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 294
           T+ V NLDP+ + + L + F   GEVK +R    ET   R + F+EF +  +   ALK L
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR-YAFVEFAEQTSVINALK-L 63

Query: 295 NRSDIAGKRIKLEPSR 310
           N +   G+ +K+  S 
Sbjct: 64  NGAMFGGRPLKVNHSN 79

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 49.8 bits (119), Expect = 8e-08
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR----HHKFIEFYDVRAAEAALKSLN 295
           L V NLDP V+ + L+QIF   G V+ ++  P K     ++ F+E++    AE AL++LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 296 RSDIAGKRIKL 306
              I    I++
Sbjct: 61  GRQIENNEIRV 71

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 49.5 bits (119), Expect = 9e-08
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           V N+    + E L +IF   G V   R     +T   + + F EF D+  A +A+++LN 
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 297 SDIAGKRIKLEPS 309
            +  G+ ++++ +
Sbjct: 63  YEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.5 bits (119), Expect = 1e-07
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 208
           TLFVRN+  +  D +L   F + G I+  +        K RGF  +++     A+ A+  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 209 LQNKPLRRRKLDIHFSIPK 227
            +      RK+ + F+  K
Sbjct: 61  KKKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHK--RHHKFIEFYDVRAAEAALKSLN 295
           L+V NL   +  + LR++F A+G + +  ++ T     R   F+ +     A+ ALK  N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 296 RSDIAGKRIKLEP 308
            S I   +I +E 
Sbjct: 63  NSFIDTSKITVEI 75

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVK--EIRETPHKRHHKFIEFYDVRAAEAALK----S 293
           L V  L PSV+  DL + F  +G V   EI +       +   + D+R +EA LK    +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 294 LNRSDIAGKRIKLEPSR 310
           LN +   G  +K+E ++
Sbjct: 62  LNGTKWKGSVLKIEEAK 78

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALK 292
           TL + NL+  +  ++L++    +F  +G V +I   +T   R   F+ F DV +A  AL+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 293 SLNRSDIAGKRIKLEPSR 310
           +L       K ++++ ++
Sbjct: 61  ALQGFPFYDKPMRIQYAK 78

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDIRAART 204
           R ++VRN++  +++ +LR +F ++G++ ++    K        + GF  +++ D  +A  
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 205 AMRALQNKPLRRRKLDI 221
           A+  L    L  RK+ +
Sbjct: 61  AL-QLNGTELGGRKISV 76

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           L V NLD +V+ + L ++F   G +   K IRE      + F+E+YD R+A AAL+++N 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE-HGNDPYAFVEYYDHRSAAAALQTMNG 59

Query: 297 SDIAGKRIK 305
             I G+ IK
Sbjct: 60  RLILGQEIK 68

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           T+ V NL  S++N DL +IF  YG+V ++     +ET   +   FI F D   A   +K+
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 294 LNRSDIAGKRIK 305
           LN  ++ G+ +K
Sbjct: 63  LNNKELFGRTLK 74

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
           TL V N  PS    D+R +F  YGE+  IR  P  R +K     +++F    +A AA+  
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIR-FPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 294 LNRSDIAGKRIKLEPSRP 311
           LN     G ++ ++ S P
Sbjct: 61  LNGKLGEGYKLVVKISDP 78

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 48.3 bits (115), Expect = 3e-07
 Identities = 19/68 (27%), Positives = 38/68 (55%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 213
           TL V N++ +V + +L  +F  YG+I+ +      R    I +YD+R+A  A++AL    
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 214 LRRRKLDI 221
           +  +++ +
Sbjct: 63  IAGKRIKL 70

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V NL  +++ +DLR IF  +GE++ ++     ET   + + FI+F D   A+ AL+ L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 295 NRSDIAGKRIKL 306
           N  ++AG+ IK+
Sbjct: 61  NGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           T+ V NL   ++ E+L++ F  +G ++E+R    K  + F+ F    AA  A+ ++N + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-GYAFVRFDTHEAAATAIVAVNGTS 60

Query: 299 IAGKRIK 305
           I G+ +K
Sbjct: 61  INGQTVK 67

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           TL + NL+ + +  DLR+ F  +GE+ +  I++      + FI++ D+ +   A++ ++ 
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 297 SDIAGKRIKL 306
             +   R+KL
Sbjct: 64  EYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 47.5 bits (114), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           L+VRN+  +V + +LR  F  YG +   R +    + RGF  + +     A  A++ L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 212 KPLRRRKL 219
             L  R L
Sbjct: 61  LVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 51.9 bits (123), Expect = 5e-07
 Identities = 32/128 (25%), Positives = 56/128 (43%), Gaps = 5/128 (3%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 281
             +         TL V NL   V+ EDLR++F  +G VK +     RET   R   F+EF
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Query: 282 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 341
               +AE A++ LN  ++ G+ ++++ ++P    R+ +          +    +  +   
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEK 224

Query: 342 ITNSPPGN 349
             N   GN
Sbjct: 225 SDNLYVGN 232

Length = 306

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKF--IEFYDVRAAEAALKS 293
           TL V NL    ++E L + F   G +K    +++   K+   F  + F     A+ AL+ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 294 LNRSDIAGKRIKLE 307
             ++   G++I +E
Sbjct: 61  KKKTKFGGRKIHVE 74

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 47.1 bits (112), Expect = 6e-07
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 239 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
           TL V   DP +   ED+ ++F  +G +        ++   F+EF D   A  AL++L+ S
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCD---IRKTFAFVEFEDSEDATKALEALHGS 57

Query: 298 DIAGKRIKLE 307
            I G  + +E
Sbjct: 58  RIDGSVLTVE 67

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 303
            L       D+ + F  YG ++EI     K    F+EF D R A+ A+  LN  ++ G+R
Sbjct: 6   RLPYRARERDVERFFKGYGRIREIN---LKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 304 IKLEPSRP 311
           + +E +R 
Sbjct: 63  VIVEHARG 70

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 46.8 bits (112), Expect = 8e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACK----HRGFVMISYYDIRAARTAMRAL 209
            L VRN+       ELR LF  +G ++++    K    HRGF  + +   + A+ AM AL
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 210 QNKPLRRRKLDIHFS 224
           ++  L  R L + ++
Sbjct: 62  KSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 47.6 bits (114), Expect = 8e-07
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-----RHHKFIEFYDVRAAEAALKS 293
           TL V  L    + E LR++F  YG+++ +R          + + F+E+   R A  A + 
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 294 LNRSDIAGKRI 304
            ++  I G  I
Sbjct: 65  AHKLVIDGSEI 75

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 52.1 bits (125), Expect = 8e-07
 Identities = 40/161 (24%), Positives = 72/161 (44%), Gaps = 14/161 (8%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           PS  + VRN+  +V +++L      +G + +       +   ++ + D  +A+  +    
Sbjct: 1   PSPVVHVRNLPQDVVEADLVEALIPFGPV-SYVMMLPGKRQALVEFEDEESAKACVNFAT 59

Query: 211 NKP--LRRRKLDIHFS----IPKDNPSDKDLNQGTLV----VFNLDPSVSNEDLRQIFGA 260
           + P  +R +    ++S    I +D  SD D      V    V N    ++ + L QIF  
Sbjct: 60  SVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNP 119

Query: 261 YGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDI 299
           YG+V  I  T  K +     +EF  V +A+ A  +LN +DI
Sbjct: 120 YGKVLRI-VTFTKNNVFQALVEFESVNSAQHAKAALNGADI 159

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). Length = 481

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V NL    + +DLR++F  YGEV ++     R T   R   F+ FYD R AE A+ ++
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 295 NRSDIAGKRIK 305
           +  ++ G+ ++
Sbjct: 61  DGKELDGRELR 71

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 51.7 bits (124), Expect = 1e-06
 Identities = 39/173 (22%), Positives = 80/173 (46%), Gaps = 11/173 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHR--GFVMISYYDIRAARTAMRA 208
           +L+V +++ +V +++L  LF+ +G    +R    +   R  G+  +++ +   A  A+  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 209 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 268
           +  K L  + + I +S  + +PS +    G + V NLD SV N+ L   F  +G +   +
Sbjct: 62  MNFKRLGGKPIRIMWS--QRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCK 119

Query: 269 ----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
               E    R + F+ F    +A+AA++ +N   +  K + +        R  
Sbjct: 120 VATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREA 172

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L+V  L   ++ E+LR +F A G ++       R T     + F+++ D   A+ A+ +L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 295 NRSDIAGKRIK 305
           N  +I  KR+K
Sbjct: 63  NGFEIRNKRLK 73

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L VF L    +  DLR++F  YG ++++     ++T   R   F+ F  V  A+ A + L
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 295 NRSDIAGKRIKLEPS 309
           N  +I G+RI+++ S
Sbjct: 62  NGMEIDGRRIRVDYS 76

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V +L P V+   L +IF   G V  IR      T     + ++ F +   AE AL +L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 295 NRSDIAGKRIKLEPS 309
           N   I GK I++  S
Sbjct: 62  NFDVIKGKPIRIMWS 76

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 208
           +LFVRNI  +    +LR  F +YG I  +Y        + RGF  + + D+R A  A+  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 209 LQNKPLRRRKLDIHFS 224
           L  K +  R+++I F+
Sbjct: 62  LDRKWICGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 5/80 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH-----HKFIEFYDVRAAEAALKS 293
            L++  L  ++++E+ R +F A G VK  +    KR        F+++     A+ A+++
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 294 LNRSDIAGKRIKLEPSRPGG 313
           LN   +  KRIK+  +RPGG
Sbjct: 62  LNGLQLQNKRIKVAYARPGG 81

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 46.5 bits (110), Expect = 2e-06
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
           +L V N+  +   EDLR+ FG YG + ++       T   R   +I+F DVR AE AL +
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 294 LNRSDIAGKRIKLE 307
           LNR  + G++I+++
Sbjct: 62  LNRKWVCGRQIEIQ 75

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-----RHHKFIEFYDVRAAEAALK 292
             ++V NL    + +D+R +F +YG++K +R  P K     R   F+EF   + A  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 293 SLNRSDIAGKRIKLE 307
           +L  + + G+R+ L+
Sbjct: 60  ALKDTHLLGRRLVLQ 74

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLN 295
           T+ V  +D S+S +DL++ F   GEV  +R    ++H     F+EF D  +A +AL +L+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL-NLS 60

Query: 296 RSDIAGKRIKLEPSR 310
            + + G  +++ PS+
Sbjct: 61  GTLLGGHPLRVSPSK 75

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           T+ V NL      +DLR++F  +G +  +     +ET   R   F+ F+    AE A++ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 294 LNR 296
           LN 
Sbjct: 61  LNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSD 298
           + + NL   V+ + L Q+F  YG V++I         +  ++F  V +AE A K+LN  +
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 299 I 299
           I
Sbjct: 64  I 64

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 20/70 (28%), Positives = 36/70 (51%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           ++V N+       EL   FE+YG +R+++ A    GF  + + D R A  A+RAL  + +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 215 RRRKLDIHFS 224
              ++ +  S
Sbjct: 62  CGNRVRVELS 71

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 49.6 bits (117), Expect = 3e-06
 Identities = 40/188 (21%), Positives = 70/188 (37%), Gaps = 26/188 (13%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 203
           +  + TLFV N+  +V + +LR LF+++G ++ +         K RGF  + +    +A 
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 204 TAMRALQNKPLRRRKLDIHFSIPKDNP--------------------SDKDLNQGTLVVF 243
            A+  L  K L  R L +  + P   P                    +        L V 
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 303
           NL    + E+L  +F + G++      P K   K  +       EA+  +L  +    K+
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSKD-GKIPKSRSFVGNEASKDALESNSRGNKK 290

Query: 304 IKLEPSRP 311
             L     
Sbjct: 291 KILGRGPR 298

Length = 306

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
           +L V N+     +EDLR+ FG YG + ++       T   R   +++F DVR AE AL +
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 294 LNRSDIAGKRIKLE 307
           L+R  I G++I+++
Sbjct: 62  LDRKWICGRQIEIQ 75

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 50.5 bits (120), Expect = 3e-06
 Identities = 38/169 (22%), Positives = 87/169 (51%), Gaps = 17/169 (10%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 209
           ++V +I+  + +  +R  F+ +G I+++  +      KH+GF  + Y    AA+ A+  +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 210 QNKPLRRRKLDIHF--SIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 262
             + L  R + +    ++P+  P    + +       + V ++ P +S  D++ +F A+G
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 263 EVK--EIRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           E+   ++   P  R HK   FIE+ ++++   A+ S+N  D+ G+ +++
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 9/75 (12%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGE---VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           L V NL  S + E LR++F  YGE   VK+I++      + F+ F +   A  A++ +N 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD------YAFVHFEERDDAVKAMEEMNG 57

Query: 297 SDIAGKRIKLEPSRP 311
            ++ G  I++  ++P
Sbjct: 58  KELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH--RGFVMISYYDIRAARTAMRAL 209
           +R L+VRN+   +   EL  LF +YG IR +        RG   + Y DI  A+ A   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 20/76 (26%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           S TL++ +++  V + +L+ LFE+YG+I+++      RG   +     + A  A++ L+N
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 212 KPLRRRKLDIHFSIPK 227
             L  +K+ + ++  K
Sbjct: 61  VKLAGKKIKVAWAPNK 76

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 44.9 bits (106), Expect = 4e-06
 Identities = 22/69 (31%), Positives = 37/69 (53%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            LVV NL  S S + L+++F     ++  +     + + F+EF     A+ AL S N ++
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 299 IAGKRIKLE 307
           I G+ I+LE
Sbjct: 63  IEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 44.9 bits (106), Expect = 4e-06
 Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 249 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           V  +D+++ FG YG++ EI     K  + F+EF D R A+ A+  LN  D+ G+R+ +E 
Sbjct: 11  VREKDIQRFFGGYGKLLEI---DLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEH 67

Query: 309 SR 310
           +R
Sbjct: 68  AR 69

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 44.8 bits (107), Expect = 4e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRAL 209
           LFV  +     + ++RALFE+YG+I  +         + +G   + +     A+ A+ AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 210 QNK 212
             K
Sbjct: 62  HGK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           TL+V +L P +S +D   +   +G   V+ +      ++  F  F + +AA  AL  L++
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60

Query: 297 SDIAGKRIKLE 307
             I GKR+ +E
Sbjct: 61  LKILGKRLVVE 71

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 18/69 (26%), Positives = 43/69 (62%), Gaps = 5/69 (7%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRH--HKFIEFYDVRAAEAALKSLNR 296
           V ++ P +S +D++ +F A+G++K      +    +H  + FIE+ + ++A+ A+ S+N 
Sbjct: 5   VASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64

Query: 297 SDIAGKRIK 305
            D+ G++++
Sbjct: 65  FDLGGQQLR 73

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA 208
            LFV  +++   + EL ALF ++G +  +         + RGF  +++  +  A  A+R 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 209 LQNKPLRRRKLDI 221
           L  K L  R + +
Sbjct: 63  LNGKELEGRVIKV 75

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 208
           L V N+       +LR +FE+YG++      R  YT  + RGF  + +YD R A  AM A
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTR-ESRGFAFVRFYDKRDAEDAMDA 59

Query: 209 LQNKPLRRRKL 219
           +  K L  R+L
Sbjct: 60  MDGKELDGREL 70

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 45.4 bits (108), Expect = 6e-06
 Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 13/105 (12%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYD-----VRAAE 288
            +VV+   PS S + ++  F ++GE+ EIR      T        I++Y       RAA+
Sbjct: 4   EIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAK 63

Query: 289 AALKSLNR---SDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDE 330
           AALK++ +     I G   K+E +        +  +L ++  +  
Sbjct: 64  AALKAVRKAQDCRIGGAEFKVELNPNERKLEKIKDKLIKQNRKKS 108

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           L+V  +      +EL   F+++G IR +      R +  I Y  I AA+ A  AL+  PL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI-DYDPGRNYAYIEYESIEAAQAAKEALRGFPL 59

Query: 215 RR--RKLDIHFS 224
               R+L + F+
Sbjct: 60  GGPGRRLRVDFA 71

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 44.1 bits (105), Expect = 6e-06
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 9/61 (14%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQN 211
           LFV N+       ELRALFE+YG +    T C   K+ GFV +   +   A  A++AL  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDVVKNYGFVHME--EEEDAEDAIKALNG 55

Query: 212 K 212
            
Sbjct: 56  Y 56

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 44.9 bits (107), Expect = 7e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMR 207
           +TLFV  +N +  +S+LR  FE+YG I+ +         K RG+  I +   R  + A +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 208 ALQNKPL--RRRKLDI 221
               K +  RR  +D+
Sbjct: 62  YADGKKIDGRRVLVDV 77

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 44.5 bits (106), Expect = 8e-06
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIR-----ETPHKRHHKFIEFYDVRAAEAAL 291
           TL++  LD   + ED+ Q   A     +K++R      T   R   F+EF  +  A   +
Sbjct: 4   TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 292 KSLNRSD---IAGKRI 304
            +LN  D   I G+ +
Sbjct: 64  DALNNLDPFVIDGRVV 79

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRA-ARTAMRALQNKP 213
           LFV N+ +++ + E + LF +YG++  ++   K +GF  I   D R  A  A   L    
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRTNAEKAKAELDGIM 61

Query: 214 LRRRKLDIHF 223
            + R+L + F
Sbjct: 62  RKGRQLRVRF 71

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 44.2 bits (105), Expect = 8e-06
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAA 290
            L + NLD  ++   L ++F  YG++K+     HK        R + F+ F     AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 291 LKSLNRSDIAGKRIKLEPSR 310
           LKSLN     GK++ +  + 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 208
           +LFVRN+       +LR  F +YG I  +Y        + RGF  I + D+R A  A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 209 LQNKPLRRRKLDIHFS 224
           L  K +  R+++I F+
Sbjct: 62  LNRKWVCGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 212
           + L+VRN+  +  + +LR LF +YG++  +    K + +  + + +   A  AM  +  K
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK---KIKDYAFVHFEERDDAVKAMEEMNGK 58

Query: 213 PLRRRKLDIHFSIP 226
            L    +++  + P
Sbjct: 59  ELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 154 TLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAM 206
           T+++ N+N  V+  EL+    A+F Q+G   DI  L T  K RG   + + DI +A  A+
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKT-LKMRGQAFVVFKDISSATNAL 59

Query: 207 RALQNKPLRRRKLDIHFS 224
           R++Q  P   + + I +S
Sbjct: 60  RSMQGFPFYDKPMRIAYS 77

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 245 LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI 304
           L+P+   +D+ + F  YG    IR+   KR   F+EF D R A+ A+  L+  ++  +R+
Sbjct: 7   LNPAAREKDVERFFKGYGR---IRDIDLKRGFGFVEFDDPRDADDAVYELDGKELCNERV 63

Query: 305 KLEPSR 310
            +E +R
Sbjct: 64  TIEHAR 69

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V NL  + + E+LR++F A+GE+ E+     +ET   +   F+ F     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 295 NRSDIAGK 302
           + S   G+
Sbjct: 62  DGSIFQGR 69

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK----RHHKFIEFYDVRAAEAALKSL 294
            L V  L  SV+ E+L ++F  +G VK +R   ++    +   ++E+ +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 295 NRSDIAGKRIKLEPSRPG 312
           + ++I  K I +  S P 
Sbjct: 64  DGTEIKEKTISVAISNPP 81

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKF-----IEFYDVRAAEAALKSL 294
           L V NL      + + + FG YGE+  +R        +      +EF    AA+AAL +L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 295 NRSDIAGKRIKLE 307
             +D+ G+ ++L+
Sbjct: 61  GGTDLLGRPVRLD 73

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 14/84 (16%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIR----TLYTACKH---RGFVMISYYDIRAARTA 205
           RT+F+RN+  +  + EL+ LF Q+G+++           H     FV   +    +A+  
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFV--KFKTKESAQKC 58

Query: 206 MRALQNKP-----LRRRKLDIHFS 224
           + A  N       L  R+L +  +
Sbjct: 59  LEAADNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK-HRGFVMISYYDIRAARTAMRALQN 211
           TL + N++  V    LR++F+ YGD++ L  T CK  + FV   ++D+R A  A+RA+  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFV--EFFDVRDAAKALRAMNG 60

Query: 212 K 212
           K
Sbjct: 61  K 61

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 156 FVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQ 210
           FV NI  +  + +L  +F + G + +          K +G+    + DI  A +A+R L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 211 NKPLRRRKLDIHFS 224
                 R L + F+
Sbjct: 62  GYEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 209
           LFVRN+     + ELR LFE +G+I  ++        + +GF  +S+     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 210 QNKPLRRRKLDI 221
                + R L +
Sbjct: 62  DGSIFQGRLLHV 73

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 294
           L +++L    +++DL Q+F  +G V   +      T   +   F+ + +  +A+AA+K++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 295 NRSDIAGKRIKLE 307
           N   + GKR+K++
Sbjct: 61  NGFQVGGKRLKVQ 73

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL 294
           +L V N+   V+   LR++F  YG+V+ ++          + FYD+R A+ A++ L
Sbjct: 3   SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVREL 58

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMR 207
           +RTLF+ N+      S+LR  FE++G+I  +    K +G    +  I Y DI +   AMR
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEI--IDIDIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 208 ALQNKPLRRRKL 219
            +  + L   ++
Sbjct: 60  KMDGEYLGNNRV 71

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 9/71 (12%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           L V NL  + ++E+LR +F  YG V E   +      +++ F+   +   AE A+K+LN 
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV------KNYGFVHMEEEEDAEDAIKALNG 55

Query: 297 SDIAGKRIKLE 307
            +  GKRI +E
Sbjct: 56  YEFMGKRINVE 66

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 43.0 bits (102), Expect = 3e-05
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
           TL V  L+   +   LR+ F  YG +K IR     +T   R + FIEF   R  +AA K 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 294 LNRSDIAGKRIKLEPSR 310
            +   I G+R+ ++  R
Sbjct: 63  ADGKKIDGRRVLVDVER 79

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 152 SRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRAL 209
           SR +FV N+N++ V   +L  +F +YG I         H+G+  + + +   AR A+   
Sbjct: 1   SR-VFVGNLNTDKVSKEDLEEIFSKYGKI----LGISLHKGYGFVQFDNEEDARAAVAGE 55

Query: 210 QNKPLRRRKLDI 221
             + +  +KLDI
Sbjct: 56  NGREIAGQKLDI 67

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHK---FIEFYDVRAAEAALKSL 294
           T+ V NLD SV  ++LR++F   GE+ ++R    +K   K   ++EF +  + + ALK L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK-L 59

Query: 295 NRSDIAGK 302
           +R  I G+
Sbjct: 60  DRELIKGR 67

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 12/73 (16%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC--------KHRGFVMISYYDIRAARTAM 206
           ++V+N+  +++D +L+ LF +YG I    T+         K +GF  +++ +  AA+ A+
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKI----TSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59

Query: 207 RALQNKPLRRRKL 219
             L  K +  +KL
Sbjct: 60  EELNGKEVNGKKL 72

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L N PL
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNMPL 62

Query: 215 RRRKLDIHF 223
           R ++L + F
Sbjct: 63  RGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
           L V NL   +S+E+L  +FG YG +++IR   T   R   F+ + D+  A+ A   L+  
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 298 DIAGK 302
           ++A +
Sbjct: 65  NVANR 69

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK---FIEFYDVRAAEAALKSL 294
           L V  L   V  + L   F  +G++K+I+       + H+   F+EF +   A AA+ ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 295 NRSDIAGKRIK 305
           N S++ G+ I+
Sbjct: 61  NESELFGRTIR 71

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVK--EIRETPHKRHHK---FIEFYDVRAAEAALKS 293
           T+ V  L  + ++E L+ +F  YG V    +    H    K   FIEF     A+ A K 
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 294 LNRSD 298
           LN   
Sbjct: 61  LNNPP 65

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTL-YTACKHRGFVMISYYDIRAARTAMRALQN 211
            TL+V  +   V + +LR  F Q+G+IR++     +   FV  ++    AA  A   L N
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFV--TFTTREAAEKAAERLFN 59

Query: 212 K 212
           K
Sbjct: 60  K 60

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAM 206
           L+V  +   V++  L A F  +GDI+ +     Y   KHRGF  + + +   A  A+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 42.3 bits (99), Expect = 5e-05
 Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 151 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAART 204
           P+ T+++ N+N  ++  EL+    A+F ++G I  +  +   K RG   + + ++ +A  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 205 AMRALQNKPLRRRKLDIHFS 224
           A+R++Q  P   + + I ++
Sbjct: 62  ALRSMQGFPFYDKPMRIQYA 81

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 42.0 bits (99), Expect = 5e-05
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHKRHHK--FIEFYDVRAAEAALKSL 294
           TL V NL+ +++ E+LR+ F  YG V++  I+  P  + +   F++F ++  A  A  ++
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 295 NRSDIAGKRIKL 306
           +   I   +IK+
Sbjct: 64  SGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 295
           TL V NL   V+   + Q+F   G  K    I +T     + F+EF++ R A A+L ++N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 296 RSDIAGKRIKL 306
              I GK +K+
Sbjct: 61  GRKIMGKEVKV 71

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--------ETPHKRHHKFIEFYDVRAAEAAL 291
           L V NL+P V+ E L Q FG +G +  ++        E    R+  F+ F +   AE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 292 KSLNRSDIAGKRIKL 306
             L+  D+ G  +KL
Sbjct: 64  DELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 240 LVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           L+V NL+   V+ + L  +FG YG+V  ++   +K+    I+  D + A+ AL  LN   
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 299 IAGKRIKLEPSR 310
           + GK++++  S+
Sbjct: 62  LHGKKLRVTLSK 73

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 209
           LFVRN+  + ++ +L  LF ++G++  ++ A      K +GF  + + D   A  A + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 210 QNKPLRRRKLDI 221
             K  + R + I
Sbjct: 65  DGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 9/66 (13%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHK--------FIEFYDVRAAEA 289
            L V NL   V+ EDL  IFG + +   E +     R           F+ F     A  
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 290 ALKSLN 295
           AL  +N
Sbjct: 63  ALNLVN 68

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAEAALKSLNRS 297
           V NL   +   D+  +F  YG +K I      R       F+EF D R AE A++  +  
Sbjct: 4   VGNLPGDIRERDIEDLFYKYGPIKAI--DLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGY 61

Query: 298 DIAGKRIKLE 307
           D  G R+++E
Sbjct: 62  DFDGYRLRVE 71

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 41.4 bits (98), Expect = 8e-05
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 7/64 (10%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQY-G--DIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           P++ LF++N+        L  LF Q+ G  ++R +      RG   + +     A  A++
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRGIAFVEFETEEQATVALQ 56

Query: 208 ALQN 211
           ALQ 
Sbjct: 57  ALQG 60

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.4 bits (98), Expect = 9e-05
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAALKS 293
           T+ + NL    + E+L+++F  +GEVK  R    K   H K   F++F    +A+  L++
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 294 LNRSD-----IAGKRIKLEPS 309
            + ++     + G+R+ +  +
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEV---KEI--RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V  L  +    DL+Q+F  YG+V   K +    +P  R   F+    V  A   ++ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 295 NRSDIAGKRIKLE 307
           +R+++ G+ I +E
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQ 210
           T+FV  ++  V + ELR+LF  +G+I  +Y      K  GFV   +    AA  A++ LQ
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEI--VYVKIPPGKGCGFV--QFVHRAAAEAAIQQLQ 58

Query: 211 NKPL 214
              +
Sbjct: 59  GTII 62

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           TL + +L   V+ EDL+ +F  YGE++ I   P  R   ++     + A  AL+ L    
Sbjct: 4   TLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-PRGCAYVCMETRQDAHRALQKLRNVK 62

Query: 299 IAGKRIKL 306
           +AGK+IK+
Sbjct: 63  LAGKKIKV 70

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins related to the La autoantigen

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 20/77 (25%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----------ETPHKRH----------HKF 278
           T+V  NL    S E+L +IFG  G VK +R           T  K            H  
Sbjct: 2   TVVAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRVGSGSTASKAKKPDTLVSNKLHAL 61

Query: 279 IEFYDVRAAEAALKSLN 295
           +E+  V AAE A+  L+
Sbjct: 62  VEYETVEAAEKAVTELS 78

This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 41.5 bits (98), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 152 SRTLFVRNINSNVED-SELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTAM 206
           SR LFV  +     D S LR LF Q G       A       RGF  + Y     A  A 
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 207 RALQNKPLRRRKLDIHFSIP 226
           +AL    L+   + + F  P
Sbjct: 62  QALNGHSLQGSPIRVSFGNP 81

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVK--EI---RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V  L+P  ++EDL  IF  +G++K  E+   ++T     + FIEF      E A   
Sbjct: 5   VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 294 LNRSDIAGKRIK 305
           ++   I  +RI 
Sbjct: 65  MDNVLIDDRRIH 76

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           TL V NL  SV +E L+  F  +G V        RET   R   +++F     A+ A+++
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 294 LNRSDIAGKRIKLEPS 309
           ++  ++ G+ I ++ S
Sbjct: 61  MDGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           TL V NL  SV+ EDL   F     +K        ET   R + F+ F  +  A+ AL  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 294 LNRSDIAGKRIKLEPSRP 311
           L    + G+ ++L+ +  
Sbjct: 61  LKNKKLHGRILRLDIAER 78

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRA 208
           TLFVRN+  +V   +L   F     I+     T     + RG+  +++  +  A+ A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 209 LQNKPL--RRRKLDI 221
           L+NK L  R  +LDI
Sbjct: 61  LKNKKLHGRILRLDI 75

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK----RHHKFIEFYDVRAAEAALKSLN 295
           ++V NL   V+ + LR+ F + GEV +++    +    R   F+ F     A+ A+K  N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 296 RSDIAGKRIKLE 307
           ++ I   +I +E
Sbjct: 63  KTFIDTSKISVE 74

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 252 EDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
           ++L++ F  +G VK +R     +T + +H+ FI+F +   A  A KS+N   + GK ++
Sbjct: 14  KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RS 297
           L V  L P  S  +L + F  +G ++ I   P +  + +IE+  + AA+AA ++L     
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN-YAYIEYESIEAAQAAKEALRGFPL 59

Query: 298 DIAGKRIKLE 307
              G+R++++
Sbjct: 60  GGPGRRLRVD 69

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           NL   + +E L+++FG YG++   +    +    +   F+ F +  AA+ A++ LN  ++
Sbjct: 8   NLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEV 67

Query: 300 AGKRI 304
            GK++
Sbjct: 68  NGKKL 72

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALK 292
           G L V NL  S   +DL ++F  +GE+ E+     K+  K     ++ F D   A  A K
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 293 SLNRSDIAGKRIKLEP 308
            L+     G+ I + P
Sbjct: 63  ELDGKVFQGRLIHILP 78

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN 295
            L + NL    + E L  +F  +   KE+R  P +R   F+EF     A  AL++L 
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQ 59

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 295
           TL V NL   V+   + Q+F   G  K    I E      + F+EFY+ R A AAL ++N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 296 RSDIAGKRIKL 306
              I GK +K+
Sbjct: 61  GRKILGKEVKV 71

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           SR +++ NI+ ++ + +LR  F QYG+I ++    + +    +++ +I  A  A+  +++
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNY-LREKNCAFVNFTNISNAIKAIDGVKS 61

Query: 212 KPLRRRKLDIHF 223
            PL  +K  I +
Sbjct: 62  HPL-FKKFKISY 72

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 5/81 (6%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 290
           ++  L+V  L  +++ E+L+ +FG+ GE+   K +R+  T     + F+ + D + AE A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 291 LKSLNRSDIAGKRIKLEPSRP 311
           + +LN   +  K IK+  +RP
Sbjct: 63  INTLNGLRLQTKTIKVSYARP 83

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           L + NL   V+  DLRQ+F  +   V  +     K  + F++  D   A+ A++ LN   
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSV--LVKKGGYAFVDCPDQSWADKAIEKLNGKI 58

Query: 299 IAGKRIKLEPSRPG 312
           + GK I++E S P 
Sbjct: 59  LQGKVIEVEHSVPK 72

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
           T+       S    D++++F   G V+++   +   + H FI F ++ AA+ A+++LN +
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 298 DIAGKRIKLE 307
            + G  IK++
Sbjct: 61  SVDGNCIKVQ 70

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 8/80 (10%)

Query: 152 SRTLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAART 204
           + T+++ N+N  ++  EL+    ALF Q+G   DI  L T  K RG   + + ++ +A  
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTM-KMRGQAFVIFKELSSATN 59

Query: 205 AMRALQNKPLRRRKLDIHFS 224
           A+R LQ  P   + + I ++
Sbjct: 60  ALRQLQGFPFYGKPMRIQYA 79

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           T+ V NL   +   ++  +F  YG + +I  +  P    + FIEF D R AE A++  + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 297 SDIAGKRIKLE 307
            D  G+R+++E
Sbjct: 61  YDFDGQRLRVE 71

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHK------FIEFYDVRAAE 288
           TL V NL+   + E L++ F   G V+ +    ++ P            F+EF    AA+
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 289 AALKSLNRSDIAGKRIKLEPS 309
            ALK L  + + G  ++L+ S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 82

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTAMRALQ 210
           + V+N+       ++R LF  YG ++++    K     RGF  + +   + A  AM AL+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 211 NKPLRRRKLDIHFS 224
           +  L  R+L + ++
Sbjct: 63  DTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           LFV N+ +++ + E + LF +YG+   ++   K +GF  I       A  A   L + P+
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFIN-KGKGFGFIKLESRALAEIAKAELDDTPM 62

Query: 215 RRRKLDIHF 223
           R R+L + F
Sbjct: 63  RGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 240 LVVFNLDPSVSNED-LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           L+V+ LD    N D L  +F  YG V  I+    K     ++  D +AAE A++ LN   
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 299 IAGKRIKLEP 308
           + G+++++  
Sbjct: 62  LFGQKLEVNF 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.5 bits (102), Expect = 3e-04
 Identities = 48/186 (25%), Positives = 82/186 (44%), Gaps = 20/186 (10%)

Query: 120 ISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI 179
           +++ AS N L      N  G+   +     +    L V  +  ++ D EL ALF   G I
Sbjct: 81  MANMASTNSL------NSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPI 134

Query: 180 RTL-----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD 234
            T      Y      G+  + +     ++ A++ L    +R ++L + ++ P    S KD
Sbjct: 135 NTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP-GGESIKD 193

Query: 235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEI---RETPHKRHHKFIEFYDVRAAEA 289
            N   L V NL  +++++ L  IFG YG++  K I   + T   R   F+ F     A+ 
Sbjct: 194 TN---LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQE 250

Query: 290 ALKSLN 295
           A+ +LN
Sbjct: 251 AISALN 256

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           ++V N+ +N   +EL   F  YG +R+++ A    GF  + + D R A  A+R L  + L
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 66

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           L V NL  +V+ E L + FG +G+++ +++    + + FI F +   A  A++ +N  ++
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 300 AGKRIKLEPSRP 311
            G+ I++  ++P
Sbjct: 61  EGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRA 208
           T+ V N++ + ++ +LR LF  +G I  +Y A      + RGF  ++++    A  A+  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 209 LQ 210
           L 
Sbjct: 61  LN 62

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 10/67 (14%)

Query: 242 VFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNRS 297
           V NL+   VS EDL +IF  YG++  I        HK   F++F +   A AA+   N  
Sbjct: 5   VGNLNTDKVSKEDLEEIFSKYGKILGI------SLHKGYGFVQFDNEEDARAAVAGENGR 58

Query: 298 DIAGKRI 304
           +IAG+++
Sbjct: 59  EIAGQKL 65

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           + V  +      ED+   F  +GE+K +     R T   + +  IE+   + A+AA++ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 295 NRSDIAGKRIK 305
           N  ++ G+ I 
Sbjct: 69  NGKELLGQTIS 79

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 9/77 (11%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGD------IRTLYT-ACKHRGFVMISYYDIRAARTAM 206
            +FV N+  + ++S L  LF  +G       IR L T  CK  GFV ++ Y+   A +A+
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAYSAI 60

Query: 207 RALQNKPLRRRKLDIHF 223
            +L    L  R L + F
Sbjct: 61  ASLNGYRLGGRVLQVSF 77

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
            L V NL   V+ EDL ++FG  GEVK+++   + R  +      + F     AE A+K 
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVK-INYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 294 LNRSDIAGKRIKLE 307
            N   + G+ +++E
Sbjct: 61  FNGVLLDGQPMQVE 74

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 248 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
            VS EDL +IF  YGE+ +I     K  + F++F    +   A+       I G+++ LE
Sbjct: 11  RVSKEDLFRIFSTYGELAQIV---LKNAYGFVQFDSPESCANAINCEQGKMIRGRKLHLE 67

Query: 308 PSRP 311
            S+P
Sbjct: 68  VSKP 71

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRGFVMISYYDIRA 201
            +  +  LFV  I  N+E+ +LR LFEQ+G I  L      YT   H+G   ++Y    +
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTG-MHKGCAFLTYCARES 59

Query: 202 ARTAMRALQNK 212
           A  A  AL  +
Sbjct: 60  ALKAQSALHEQ 70

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 39.2 bits (91), Expect = 5e-04
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 240 LVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           L+V NL+P +++   L  +FG YG+V  ++   +K+ +  ++  D   A+ A+  LN   
Sbjct: 3   LLVSNLNPDAITPHGLFILFGVYGDVHRVKIMFNKKENALVQMADATQAQLAMSHLNGQR 62

Query: 299 IAGKRIKLEPSR 310
           + GK I+   S+
Sbjct: 63  LYGKVIRATLSK 74

This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 76

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 24/72 (33%), Positives = 30/72 (41%), Gaps = 12/72 (16%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMR 207
           LFV N++    + ELRA F + G IR +          CK   FV     D      A  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFV-----DFEEIEFATN 55

Query: 208 ALQNKPLRRRKL 219
           AL+ K L  R L
Sbjct: 56  ALKGKHLNGRAL 67

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

 Score = 39.6 bits (92), Expect = 6e-04
 Identities = 25/92 (27%), Positives = 52/92 (56%), Gaps = 7/92 (7%)

Query: 240 LVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  LN   
Sbjct: 2   LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQK 61

Query: 299 IAGKRIKLEPSRPGGARRNLMLQLNQELEQDE 330
           + GK +++  S      ++  +QL +E ++D+
Sbjct: 62  LHGKPLRITLS------KHQTVQLPREGQEDQ 87

This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. . Length = 93

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDI 299
           V NL P +  +D+  +F  YG +++I +  ++R     F+EF D R AE A+   +  D 
Sbjct: 4   VGNLPPDIRTKDIEDLFYKYGAIRDI-DLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYDY 62

Query: 300 AGKRIKLEPSR 310
            G R+++E  R
Sbjct: 63  DGYRLRVEFPR 73

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.1 bits (92), Expect = 6e-04
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 252 EDLRQIFGAYGEVKEIR-ETPHKRHHK-------FIEFYDVRAAEAALKSLN 295
           ED+++  G YG+V  +    P             F+EF DV  A+ A  +L 
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 39.2 bits (92), Expect = 7e-04
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTA 205
           P  TLFV  ++    +  LR +F +YGDIR L           +G+  + Y   R A  A
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 206 MRALQN 211
            R    
Sbjct: 62  YRDAHK 67

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIR--ETPHKRHHKFIEFYDVRAAEAALKSL 294
           L+V  L  +++ +++R +F + GE+   K IR   T     + F+ + D   AE A+ +L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 295 NRSDIAGKRIK 305
           N   +  K IK
Sbjct: 64  NGLRLQNKTIK 74

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 240 LVVFNLDPSVSN-EDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
           L++ NL  S+     L++IFG YG+V+E    P KR  K     F+     + AE AL++
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREA-TIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61

Query: 294 LNRSDIAGKRIKLE 307
            N  +I G+ + ++
Sbjct: 62  TNGLEIDGRPVAVD 75

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
           T+ +FN+  +V+ E ++  F   G +V++I   P       +EF     A  A  SLN S
Sbjct: 2   TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDH-EGALVEFESPSDAGKASLSLNGS 60

Query: 298 DIAGKRIKL 306
              GK IK+
Sbjct: 61  QFGGKTIKI 69

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           V N+D   + E+L++ F + G +  I     + T   +   +IEF D  + E AL  LN 
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNE 62

Query: 297 SDIAGKRIK 305
           S+  G++IK
Sbjct: 63  SEFRGRQIK 71

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSL 294
           TL V NL P+ + E+LRQ+F      + ++   H +      F+EF DV  A  AL SL
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGFRRLKM--HNKGGGPVCFVEFEDVSFATQALNSL 60

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 38.4 bits (89), Expect = 7e-04
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 155 LFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 212
           +F+ N+N+  V+ S++ A+F +YG I      C  H+GF  + Y + R AR A+     +
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKI----VGCSVHKGFAFVQYVNERNARAAVAGEDGR 59

Query: 213 PLRRRKLDIHFS 224
            +  + LDI+ +
Sbjct: 60  MIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 301
           V N+  + ++++LR +F  +G V E  +    + + F+       A AA+++LN  ++ G
Sbjct: 5   VGNVSATCTSDELRGLFEEFGRVVECDKV---KDYAFVHMEREEEALAAIEALNGKEVKG 61

Query: 302 KRIKLE 307
           +RI +E
Sbjct: 62  RRINVE 67

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 300
            LD SV+ + L + F  YG V  +   R    +R    + F  V AA+AA+  +    + 
Sbjct: 14  GLDESVTEQYLTRHFSRYGPVVHVVIDR----QRGQALVFFDKVEAAQAAVNEMKGRKLG 69

Query: 301 GKRIKL 306
           G+++++
Sbjct: 70  GRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA-AEAALKSLNRSD 298
           L V NL   ++ E+ +++F  YGEV E+     ++   FI   D R  AE A   L+   
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRTNAEKAKAELDGIM 61

Query: 299 IAGKRIK 305
             G++++
Sbjct: 62  RKGRQLR 68

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMR 207
           +RTLFV N+   + + ELR  FE+YG +  +      RG    +  + + ++  A  A  
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 208 ALQNKPLRRRKLDI 221
           A+  + + R ++ I
Sbjct: 62  AMSGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 42.7 bits (100), Expect = 8e-04
 Identities = 33/134 (24%), Positives = 63/134 (47%), Gaps = 16/134 (11%)

Query: 187 KHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQGTLVVF- 243
           K+RGF  + Y   RAA  A R L    ++     + + ++ P++   D+D+     +++ 
Sbjct: 180 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEV-DEDVMAKVKILYV 238

Query: 244 -NLDPSVSNEDLRQIF-----GAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
            NL  + + E + + F     G    VK+IR+      + F+ F D   A  A+  LN  
Sbjct: 239 RNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD------YAFVHFEDREDAVKAMDELNGK 292

Query: 298 DIAGKRIKLEPSRP 311
           ++ G  I++  ++P
Sbjct: 293 ELEGSEIEVTLAKP 306

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           V +L P +  E LR  F  +GE+ + R     +T   + + F+ F     AE A++S+N 
Sbjct: 4   VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

Query: 297 SDIAGKRIK 305
             + G+ I+
Sbjct: 64  QWLGGRAIR 72

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            + V  L    +++ LR+ F  +GE++E      R+T   R + F+ F D  +AE A K 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 294 LNRSDIAGKRIKLE 307
            N   I G++  + 
Sbjct: 62  PNPI-IDGRKANVN 74

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 38.6 bits (89), Expect = 9e-04
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 5/81 (6%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 290
           ++  L+V  L  +++ E+ R +FG+ GE+   K +R+  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 291 LKSLNRSDIAGKRIKLEPSRP 311
           + +LN   +  K IK+  +RP
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 154 TLFVRNINSNVEDSELRALFEQYG---DIRTLY---TACKHRGFVMISYYDIRAARTAMR 207
            L+V N+  NV + +L+ LF Q+G     R +    T  + RGF  +       A  A+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETG-RSRGFGFVEMETAEEANAAIE 59

Query: 208 ALQNKPLRRRKL 219
            L       R L
Sbjct: 60  KLNGTDFGGRTL 71

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIR------TLYTACKHRGFVMISYYDIRAARTAM 206
             +FV  +  +  D  LR  F Q+G+I          T  K RG+  +++ D  +   A 
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTG-KSRGYGFVTFKDKES---AE 56

Query: 207 RALQN 211
           RA ++
Sbjct: 57  RACKD 61

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKF--IEFYDVRAAEAALKSL 294
           TL V NL  S   +DL + F   GEV ++R  +    R   F  +EF     A+ AL+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-K 59

Query: 295 NRSDIAGKRIKLE 307
           +  ++ G+ I+++
Sbjct: 60  SGEELLGREIRVD 72

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           + V N+D   S E+LR +F AYG V         R   F+      AA+ A++ LN  ++
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM---RQFAFVHLRGEAAADRAIEELNGREL 59

Query: 300 AGKRIKLEPS 309
            G+++ +E S
Sbjct: 60  HGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP) and similar proteins

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHHKF--IEFYDVRAAEAALK 292
            L V NLD  +S ++L+Q     F  +G+V  +   P         +   +++ A+ A+ 
Sbjct: 6   DLQVSNLDYRLSRKELQQTLTNQFKRHGKVLSVSLRPQTDGSLVASVRVPNLQDAQYAIS 65

Query: 293 SLNRSDIAGKRIKLEPSRPGG 313
            L+R  I  KRI +  ++   
Sbjct: 66  QLHRRKIGSKRILVSYAQGSS 86

This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. Length = 89

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRAL 209
           + L V NI     D +LR +F Q+G   D+  ++     +GF  +++ +   A  A   L
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 210 QNKPLRRRKLDIH 222
               +  RK++++
Sbjct: 61  HGTVVEGRKIEVN 73

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 268
             LVV NL PSV+ +D+ ++F A G +K  R
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRAR 31

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYT---ACKHRGFVMISYYDIRAART 204
           P+R +FV  I  +  + ELR  F ++G   D++ +       K  GFV  ++     A  
Sbjct: 2   PNR-IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFV--TFETQEDAEK 58

Query: 205 AMRALQNKPLRRRKLDI 221
              A+ N   R +KL+I
Sbjct: 59  I-LAMGNLNFRGKKLNI 74

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 10/80 (12%)

Query: 239 TLVVFNLDPSVSNED----LRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEA 289
           T+ V   D S+  +D    L + F + GE+  +     RET   +   +IEF  V   E 
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 290 ALKSLNRSDIAGKRIKLEPS 309
           AL+ L+ SD+ G  + ++ +
Sbjct: 61  ALE-LDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIR-TLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           +RTLFV+N+  N+   EL+ +FE   DIR         +G   I+Y + +    A +AL+
Sbjct: 3   ARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKG---IAYIEFKTEAEAEKALE 59

Query: 211 NK 212
            K
Sbjct: 60  EK 61

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMI-----SYYDIRAARTAMRAL 209
           LFV N+ +++ + + + LFE+YG+   ++   + RGF  I     +  +I  A      L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 62

Query: 210 QNKPLRRR 217
           +N+PLR R
Sbjct: 63  KNRPLRIR 70

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKF--IEFYDVRAAEAAL----K 292
           T+ V NL    +   +RQ F   GE++E+ +           IEF     A AAL    K
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREV-KIVESEGGLVAVIEFETEDEALAALTKDHK 60

Query: 293 SLNRSDIA 300
            L  ++I+
Sbjct: 61  RLGGNEIS 68

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L +  L     +  LR  F  +G+V +      RET   R   F+ F D  AA AA+  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 295 NRSDIAGKRIKLEPS--RPGGAR 315
           +  ++ G+ I++ P+  RP   R
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPR 119

Length = 144

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 254 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
           +RQ F  +G++ EIR  P K  + FI F    +A  A+ S+N + I G  +K
Sbjct: 17  MRQTFSPFGQIMEIRVFPEK-GYSFIRFSTHESAAHAIVSVNGTTIEGHVVK 67

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 15/157 (9%)

Query: 195 SYYDIRAARTAMRALQNKPLR------RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 248
            YY  R  R+  R+             RR         K+  ++ + +  T+ V  L   
Sbjct: 41  DYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALK 100

Query: 249 VSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKR 303
               DL + F   G+V++++    +   +     ++EFYDV +   AL +L    + G+ 
Sbjct: 101 ARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRP 159

Query: 304 IKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGS 340
           I ++ S+   A +N   +       D    L+  VG+
Sbjct: 160 IIVQSSQ---AEKNRAAKAATHQPGDIPNFLKLYVGN 193

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 207
             L V  +  ++   ELR+LFE  G I +          +  G+  + Y D   A+ A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 208 ALQNKPLRRRKLDIHF 223
            L    +R ++L + +
Sbjct: 61  TLNGFEIRNKRLKVSY 76

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRAL 209
            LFV  +  +V   EL  LF+++G ++++      + K +G   + Y +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 210 QNKPLRRRKLDIHFSIP 226
               ++ + + +  S P
Sbjct: 64  DGTEIKEKTISVAISNP 80

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 9/63 (14%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQN 211
           LFV N+     + E+R+LFEQYG +      C   K+ GFV +   D  AA  A+R L +
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKV----LECDIIKNYGFVHMD--DKTAADEAIRNLHH 56

Query: 212 KPL 214
             L
Sbjct: 57  YKL 59

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 253 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 312
           D+ + F  YG++ E+     K  + F+EF D+R A+ A+  LN  D+ G+R+ +E +R  
Sbjct: 15  DVERFFKGYGKILEV---DLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHAR-- 69

Query: 313 GARRN 317
           G RR+
Sbjct: 70  GPRRD 74

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast sporulation-specific protein 2 (Ssp2) and similar protein

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 247 PSVSN-EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKR 303
           PS  + E+L+  F  +GE+ +I     ++    I F D+R+A  A ++L    S +  K 
Sbjct: 3   PSDFDVEELKDDFTVFGEIVDISPIISRKLCVSIFFADIRSAIRAKETLEDKGSSLNNKY 62

Query: 304 IK 305
           IK
Sbjct: 63  IK 64

This subfamily corresponds to the RRM of the lineage specific yeast sporulation-specific protein 2 (Ssp2) and similar proteins. Ssp2 is encoded by a sporulation-specific gene necessary for outer spore wall assembly in the yeast Saccharomyces cerevisiae. It localizes to the spore wall and may play an important role after meiosis II and during spore wall formation. Ssp2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 294
           L V NL   ++ ++L++ F  +G V E+R        +     F+ F D  A +  L + 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 295 NRSDIAGKRIKLEPSR 310
                   R+ +E  +
Sbjct: 66  PIYFRGDHRLNVEEKK 81

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAARTAMRA 208
           + VRNI       ELR LF  +G+++T+    K      HRGF  + +   + A+ A +A
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 209 LQ 210
           L 
Sbjct: 63  LC 64

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 15/79 (18%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           R +F  N   +   SE+  LF +YG     D+++        GF  +   D R A  A+R
Sbjct: 1   RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKS--------GFAFVYMEDERDAEDAIR 52

Query: 208 ALQNKPL--RRRKLDIHFS 224
            L N     +RR+L + ++
Sbjct: 53  GLDNFEFGRQRRRLRVEWA 71

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 238 GTLVVFNL-DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
             L+V NL +  V+ + L  +FG YG+V+ ++   +K+    I+  D   ++ A+  LN 
Sbjct: 14  TVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNG 73

Query: 297 SDIAGKRIKLEPSR 310
             + GK I++  S+
Sbjct: 74  QKMYGKIIRVTLSK 87

This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 107

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 301
           V NL       +L + F  YG ++ +    +     F+EF D R AE A++ L+   I G
Sbjct: 4   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 63

Query: 302 KRIKLEPSRPGGARR 316
            R+++E S  G  RR
Sbjct: 64  SRVRVELS-TGMPRR 77

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           +  +F ++  +    +R  F  +G+ K +    H+    F+ F    AAE    +++ + 
Sbjct: 4   SFFLFGVEDDLPEYKIRDYFEQFGKSKSVI-VNHRAKCGFVRFETREAAEKFAAAISENG 62

Query: 299 IA 300
           + 
Sbjct: 63  LN 64

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 154 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           T++V N+   + + EL+  F  +G   ++R      K +G+  + +    AA TA+ A+ 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF----KDKGYAFVRFDTHEAAATAIVAVN 57

Query: 211 NKPL 214
              +
Sbjct: 58  GTSI 61

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 208
           +FV +++  ++   LRA F  +G+I      + + T  K +G+  +S+     A  A+++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTG-KSKGYGFVSFVKKEDAENAIQS 60

Query: 209 LQNKPLRRRKL 219
           +  + L  R +
Sbjct: 61  MNGQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 12/46 (26%), Positives = 25/46 (54%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD 198
           R +FV  +  ++ + +LR  F Q+G++  +Y     R F  +++ D
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFAD 46

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 239 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
           TL V N DP +    DL + F  YG++  +R    +R+  F+++     A  AL+S N S
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRI---RRNFAFVQYETQEDATKALESTNMS 57

Query: 298 DIAGKRIKLE 307
            +  + I +E
Sbjct: 58  KVLDRVISVE 67

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           V NLD  V+ E L ++F   G V  +     R T   + + F+EF     A+ A+K +N 
Sbjct: 3   VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62

Query: 297 SDIAGKRIKL 306
             + GK I++
Sbjct: 63  IKLYGKPIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAEAALKSLN 295
           L V NL  +V  E + + F  YG V+ ++  P +        F++F D+++A+ A  ++N
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61

Query: 296 RSD 298
           +  
Sbjct: 62  KMG 64

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 155 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH-RGFVMISYYDIRAARTAMRALQ 210
           +FV  I  ++ + EL  LFE+ G   ++R +       RG+  ++Y +  AA+ A++ L 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 211 NKPLRRRKL 219
           N  +R  K 
Sbjct: 64  NYEIRPGKR 72

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           V N+    + E L+ IF   G V        RET   + + F E+ D   A +A+++LN 
Sbjct: 3   VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62

Query: 297 SDIAGKRIKLE 307
            ++ G++++++
Sbjct: 63  YELNGRQLRVD 73

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRA 208
             ++FV  ++ +V   EL   F ++G   ++  +  A     F  I +   +AA  A+ +
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62

Query: 209 -----LQNKPLR 215
                L+NK + 
Sbjct: 63  ENHSMLKNKTMH 74

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 248 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK 302
           + + ED+R +F  YG ++E+     ++T   +   F++F     A+ A+++L+     GK
Sbjct: 10  TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH-----GK 64

Query: 303 RIKLEPSRP 311
                 SRP
Sbjct: 65  VTMPGASRP 73

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 20/68 (29%), Positives = 36/68 (52%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 301
           V NL  + +  +L + FG YG ++ +    +     F+EF D R A  A++ L+   + G
Sbjct: 9   VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 68

Query: 302 KRIKLEPS 309
            R+++E S
Sbjct: 69  CRVRVELS 76

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           +FV N++ +    ELRALFE YG    + +    R F  +      AA  A+  L  + L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYG---AVLSCAVMRQFAFVHLRGEAAADRAIEELNGREL 59

Query: 215 RRRKLDIHFS 224
             RKL +  S
Sbjct: 60  HGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           ++V N+ +     EL   F  YG +RT++ A    GF  + + D R A  A+R L  K +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 215 --RRRKLDIHFSIPK 227
              R ++++   +P+
Sbjct: 62  CGSRVRVELSTGMPR 76

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR----HHKFIEFYDVRAAEAALKSL 294
            L V NL P VSNE L Q F  +GEV+        R        +EF     A+AA+K  
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRC 60

Query: 295 N 295
           +
Sbjct: 61  S 61

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDI 179
           RT+FV N+    +  +L+ LF+Q+G I
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPI 27

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 21/84 (25%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMIS--------Y----YDIRA 201
            L V N+     D + R L   +G +         R F++ S        Y    Y  +A
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAV--------ERCFLVYSESTGESKGYGFVEYASKA 52

Query: 202 -ARTAMRALQNKPLRRRKLDIHFS 224
            A  A   L  K +  RKL + ++
Sbjct: 53  SALKAKNQLDGKQIGGRKLQVDWA 76

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAALKSL 294
           L+V  L  +++ ++LR +F + GEV   K IR+    H   + F+ + + + AE A+ +L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 295 NRSDIAGKRIKLEPSRP 311
           N   +  K IK+  +RP
Sbjct: 64  NGLRLQSKTIKVSYARP 80

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 213
           L +RN+  +V +S+L AL   +G +   L    K++  V      + +A++ +      P
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALV--EMDSVESAKSMVDYYLTVP 59

Query: 214 LRRRKLDIHF 223
              R   ++ 
Sbjct: 60  ALIRGRRVYI 69

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 245 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           L    + E LR+ F  YGEV +        T   R   F+ F D  + +  L +
Sbjct: 6   LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE--TPHKRHHKFIEFYDVRAAEAALKS 293
           TL + +L+P +    +   F   GE   VK IR   T     + F+EF    AAE AL+S
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 294 LNRSDIAGK 302
           LN   I   
Sbjct: 61  LNGKPIPNT 69

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           ++ V       S E L   F A+G V  +     K  +  +EF      +  L     + 
Sbjct: 4   SVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSEPQHT- 62

Query: 299 IAGKRIKLEP 308
           + G R+++ P
Sbjct: 63  LNGHRLRVRP 72

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	818
KOG4660	549	consensus Protein Mei2, essential for commitment t	100.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.91
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.89
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.88
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.87
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.87
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.83
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.81
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.75
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.74
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.73
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.71
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.71
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.69
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.67
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.65
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.61
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.6
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.59
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.54
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.49
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.49
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.45
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.44
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.42
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.41
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.39
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.39
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.33
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.31
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.3
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.28
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.26
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.26
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.26
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.25
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.24
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.23
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.17
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.17
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.13
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.13
KOG0122	270	consensus Translation initiation factor 3, subunit	99.13
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.12
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.12
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.12
PLN03120	260	nucleic acid binding protein; Provisional	99.1
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.09
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.09
smart00362	72	RRM_2 RNA recognition motif.	99.07
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.07
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.06
PLN03120	260	nucleic acid binding protein; Provisional	99.06
KOG0122	270	consensus Translation initiation factor 3, subunit	99.06
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.04
PLN03213	759	repressor of silencing 3; Provisional	99.04
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.04
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.02
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.99
smart00362	72	RRM_2 RNA recognition motif.	98.97
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.96
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.95
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.95
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.93
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.92
smart00360	71	RRM RNA recognition motif.	98.91
PLN03121	243	nucleic acid binding protein; Provisional	98.9
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.89
PLN03213	759	repressor of silencing 3; Provisional	98.88
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.85
PLN03121	243	nucleic acid binding protein; Provisional	98.85
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.85
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.83
smart00360	71	RRM RNA recognition motif.	98.83
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.81
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.8
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.76
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.76
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.73
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.73
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.72
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.7
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.67
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.66
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.65
smart00361	70	RRM_1 RNA recognition motif.	98.63
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.62
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.57
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.56
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.55
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.45
smart00361	70	RRM_1 RNA recognition motif.	98.44
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.41
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.4
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.33
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.28
KOG4210	285	consensus Nuclear localization sequence binding pr	98.26
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.24
KOG0226	290	consensus RNA-binding proteins [General function p	98.2
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.15
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.13
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.09
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.07
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.07
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.02
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.97
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.96
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.95
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.91
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.9
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.87
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.86
KOG0151	877	consensus Predicted splicing regulator, contains R	97.86
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.83
KOG0151	877	consensus Predicted splicing regulator, contains R	97.83
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.69
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.69
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.61
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.51
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.49
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.48
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.46
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.44
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.43
KOG4210	285	consensus Nuclear localization sequence binding pr	97.34
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.31
KOG0226	290	consensus RNA-binding proteins [General function p	97.29
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.19
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.12
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.03
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.61
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.52
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.44
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.41
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.39
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.35
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.3
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.23
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.18
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	96.18
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.16
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.62
KOG3152	278	consensus TBP-binding protein, activator of basal	95.56
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.52
KOG2314	698	consensus Translation initiation factor 3, subunit	95.37
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.95
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.91
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.79
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.69
KOG3152	278	consensus TBP-binding protein, activator of basal	94.51
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.48
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.26
KOG2314	698	consensus Translation initiation factor 3, subunit	94.18
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	93.51
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.24
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.98
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	92.73
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	92.66
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	92.32
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.74
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	91.64
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.0
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	90.92
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	90.8
KOG2135	526	consensus Proteins containing the RNA recognition	90.76
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.45
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	89.88
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	89.86
KOG1996	378	consensus mRNA splicing factor [RNA processing and	89.83
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	89.69
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	89.06
KOG2068	327	consensus MOT2 transcription factor [Transcription	87.69
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	87.18
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	85.7
KOG2068	327	consensus MOT2 transcription factor [Transcription	83.9
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	82.56
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	82.09

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=100.00  E-value=6e-75  Score=639.89  Aligned_cols=518  Identities=53%  Similarity=0.791  Sum_probs=390.7

Q ss_pred             HHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhccccCccccCCCCccccCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q 003463           90 EDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSEL  169 (818)
Q Consensus        90 el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~~~~~~~l~n~~~~~~g~~~~~e~~srtLfV~NLP~~vTEeeL  169 (818)
                      +++++|...|++++..+.......   ..              ...+....+.+++|..+  +++ +|         .+|
T Consensus         2 ~d~~lf~~~G~~el~~~~~~~~~~---~~--------------~~~n~~~~~~~~~P~~~--s~~-~~---------~~l   52 (549)
T KOG4660|consen    2 EDCDLFSSGGGMELDADSFDNLSV---RN--------------SDRNSAGFVFPEHPPGE--SRT-FV---------SEL   52 (549)
T ss_pred             CccccccCCCCCCcccccccchhh---cc--------------cccCCCccccCCCCCCC--CCC-Ch---------hhH
Confidence            567899999999877665433222   10              11244557778888887  666 77         678


Q ss_pred             HHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCCCCCCccceeeecCCCCC
Q 003463          170 RALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV  249 (818)
Q Consensus       170 r~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~v  249 (818)
                      -.+|+.|                                  +..+           +.+++.+++.++++|+|.|||.+|
T Consensus        53 ~a~f~~~----------------------------------~~p~-----------~~~np~~~~~~~~~L~v~nl~~~V   87 (549)
T KOG4660|consen   53 SALFEPF----------------------------------NKPL-----------RPDNPSEKDMNQGTLVVFNLPRSV   87 (549)
T ss_pred             Hhhhhcc----------------------------------CCCC-----------CcCCCCcccCccceEEEEecCCcC
Confidence            8889888                                  1111           115566778889999999999999


Q ss_pred             CHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcccchhhhccchhccHH
Q 003463          250 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQD  329 (818)
Q Consensus       250 teedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r~~~~~ql~~~~~~~  329 (818)
                      ++++|+++|+.||+|+.|+.+...++.+||+|.|+++|++|+++|++.++.|++|+    ++.+.+++.+-+..      
T Consensus        88 sn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k----~~~~~~~~~~~~~~------  157 (549)
T KOG4660|consen   88 SNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK----RPGGARRAMGLQSG------  157 (549)
T ss_pred             CHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc----CCCcccccchhccc------
Confidence            99999999999999999999999999999999999999999999999999999999    77777776665554      


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCccCCCCCCCCccccccCCCCCCCCCCCcCCCCCCCcccCCCCCCccccccccCCccCcc
Q 003463          330 ESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRG  409 (818)
Q Consensus       330 ~l~~~f~~~GsP~a~s~P~~~~~~~~p~~~~~~~~~~~~~~~~~~sP~~~~~~~g~~s~~~~~~~~~~~~~~~~~~~~~~  409 (818)
                        ..+..++++|.++++|+.|.+               .+.+..++|.....       ++...++ +-....+...+.-
T Consensus       158 --~~~~~~~~~p~a~s~pgg~~~---------------~~~~g~l~P~~s~~-------~~~~~~~-~~~~~~~~~~~~~  212 (549)
T KOG4660|consen  158 --TSFLNHFGSPLANSPPGGWPR---------------GQLFGMLSPTRSSI-------LLEHISS-VDGSSPGRETPLL  212 (549)
T ss_pred             --chhhhhccchhhcCCCCCCcC---------------Ccceeeeccchhhh-------hhhcchh-ccCccccccccch
Confidence              557789999999999999961               12233355654332       2222111 1111111222222


Q ss_pred             cchhhhhccccccCCCccccCCCCCCCcCCccCCccCCCCCCCCCCCCcccCCCCcccCCCCCCCCCCCCCCcccCCCCC
Q 003463          410 SLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMG  489 (818)
Q Consensus       410 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~  489 (818)
                      .|  |.|.+      ....-+|+++++..          |..+++..++.+++++--+|                     
T Consensus       213 ~h--q~~~~------~~~~~s~a~~~~~~----------G~~~s~~~~v~t~S~~~g~~---------------------  253 (549)
T KOG4660|consen  213 NH--QRFVE------FADNRSYAFSEPRG----------GFLISNSSGVITFSGPGGVW---------------------  253 (549)
T ss_pred             hh--hhhhh------hccccchhhcccCC----------ceecCCCCceEEecCCCccc---------------------
Confidence            23  33332      11124567777632          56677777888888774444                     


Q ss_pred             CCCCCCCccCCCCCCCCCCCCCCCccccCcCCCCCCCCcccccCCCCCCCCCcCCCCccccCCCCCCCCCccccccCCCc
Q 003463          490 HPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRA  569 (818)
Q Consensus       490 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gsap~~~~~~~~~~~~~~s~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  569 (818)
                      +++...         .........+++||||+||+                  ..+....+++++.+..+++.++.+.  
T Consensus       254 n~~~~~---------r~~~~~~~~~~~~hi~~~Ps------------------~~~l~~~~~~~f~~~s~~~~~~~~~--  304 (549)
T KOG4660|consen  254 NPFPSR---------RQRQNSSSSHYEHHIGSAPS------------------MHHLLSRISVGFNGGSGALEMNSNG--  304 (549)
T ss_pred             CCcccc---------ccccccCcccccCccCCCcc------------------cccccccCccccCCCCCCccccccc--
Confidence            122111         11222344567999999996                  1223345567777777776554322  


Q ss_pred             CCCCC-ccCCCCCCCCCCc-ccccCCCCCCCcccCCCCCCCCCCCccccccc---cccccccccCCCCccccccccccch
Q 003463          570 SVNPG-ITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYE---RGRSRRIENNNGNQLDSKKQFQLEL  644 (818)
Q Consensus       570 ~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---r~r~rr~~~~~~~~~~~~~~~~~~~  644 (818)
                      ..|-| .+..+++.+..+. +++.+.++..+.|-+++.+.    ...+...+   ..+.||.+. ...+ ...+++.+|+
T Consensus       305 ~~n~g~~~~t~~~~e~~s~n~~~e~~~rv~~~f~~~~~~~----~~~~~~~~~~~~~~~~Rtt~-~i~n-i~n~~~~~dl  378 (549)
T KOG4660|consen  305 QANQGFLTKTGNVTEFNSKNVGMESSPRVPKNFEGRRSYT----SQNDYPVELILNYRDRRTTV-MIKN-IPNKYGQLDL  378 (549)
T ss_pred             cCCCCccccCcccccccCCCccccccCCCCcccccccccc----cccccccccccccccchhhh-hhhc-cccchhHHHH
Confidence            33444 4678899888886 99999999999999888653    33444444   677788886 3333 3489999999


Q ss_pred             hhHhcCCCcceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCccc
Q 003463          645 EKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWE  724 (818)
Q Consensus       645 ~~i~~g~d~rTtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~  724 (818)
                      .+|.+|+|.|||+||||||||||++||++. ||.++|+|||+||||||+|+||||||||||++|+++++||++|||++|+
T Consensus       379 ~~Ildge~~rtt~~iknipNK~T~~ml~~~-d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~  457 (549)
T KOG4660|consen  379 LRILDGECPRTTLMIKNIPNKYTSKMLLAA-DEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWE  457 (549)
T ss_pred             HHHHhCcCchhhhHhhccCchhhHHhhhhh-hccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchh
Confidence            999999999999999999999999999999 9999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccEEEEEeeecccHHHHHHHhccCcccCCCCCccceEEcCCCCCCCCccccccCCCCCCcccccCCCCC
Q 003463          725 KFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQEQLNSNSVNFQVCPSNGS  797 (818)
Q Consensus       725 ~~~s~k~~~~~~A~iQg~~~l~~~~~~s~~~~~~~~~~p~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  797 (818)
                      +|+|+|||+|+|||||||++|++|||||++|||++.|+|++|++  ++.|.   +|++|... +++.+....+
T Consensus       458 ~FnS~Kia~itYArIQGk~~Li~hFqnS~lm~E~e~y~Pvvf~p--p~dg~---~~~~p~~~-~~~a~~~~s~  524 (549)
T KOG4660|consen  458 KFNSEKIASITYARIQGKEALIEHFQNSSLMCEDEAYRPVVFSP--PEDGR---EEPEPVKL-NQDAGAGHST  524 (549)
T ss_pred             hhcceeeeeeehhhhhchHHHHHHhhcccccccchhcCceEecC--ccccc---ccCccccc-cccCCCCccc
Confidence            99999999999999999999999999999999999999999998  77777   99999988 8776655443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=100.00  E-value=2.5e-46  Score=336.92  Aligned_cols=97  Identities=67%  Similarity=1.202  Sum_probs=96.4

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCcccCCCCccEEE
Q 003463          654 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVAS  733 (818)
Q Consensus       654 rTtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~s~k~~~  733 (818)
                      |||||||||||||||+||+++||+.++|+||||||||||+++||+|||||||+++++|.+|+++|+|++|+.++|+|||+
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeecccHHHHHHHhc
Q 003463          734 LAYARIQGRAALVAHFQ  750 (818)
Q Consensus       734 ~~~A~iQg~~~l~~~~~  750 (818)
                      |+||||||++|||+|||
T Consensus        81 i~yAriQG~~alv~~f~   97 (97)
T PF04059_consen   81 ISYARIQGKDALVEHFR   97 (97)
T ss_pred             EehhHhhCHHHHHHhhC
Confidence            99999999999999997

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=4.4e-32  Score=300.25  Aligned_cols=241  Identities=18%  Similarity=0.291  Sum_probs=199.6

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  146 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~  146 (818)
                      -++++|++||.+++|.++.++|+.+|.|   .|..|..+++++||+||.|.+.+.|.    .+++..+.+...++....+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            3689999999999999999999999987   57888889999999999999877554    4556666665555544433


Q ss_pred             CC-CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccc--cc
Q 003463          147 YG-EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RK  218 (818)
Q Consensus       147 ~~-e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~  218 (818)
                      .. ....++|||+|||.++++++|+++|++||.|..+++     .+.++|||||+|.+.++|++|++.|+|..+.|  .+
T Consensus        83 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~  162 (352)
T TIGR01661        83 SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEP  162 (352)
T ss_pred             cccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCcee
Confidence            32 235679999999999999999999999999988773     45689999999999999999999999998876  56


Q ss_pred             ccccccCCCCCCCC----------------C-------------------------------------------------
Q 003463          219 LDIHFSIPKDNPSD----------------K-------------------------------------------------  233 (818)
Q Consensus       219 L~V~~a~pk~~~~~----------------~-------------------------------------------------  233 (818)
                      |.|.++........                .                                                 
T Consensus       163 i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (352)
T TIGR01661       163 ITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQ  242 (352)
T ss_pred             EEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccc
Confidence            77777643220000                0                                                 


Q ss_pred             -----------------------CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHH
Q 003463          234 -----------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVR  285 (818)
Q Consensus       234 -----------------------~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e  285 (818)
                                             .....+|||+|||+++++++|+++|++||.|+++++     ++.++|||||+|.+.+
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~  322 (352)
T TIGR01661       243 RASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD  322 (352)
T ss_pred             cCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHH
Confidence                                   000125999999999999999999999999999976     5678999999999999


Q ss_pred             HHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          286 AAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       286 ~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      +|.+|+..|||..|.||+|+|.|..++..
T Consensus       323 ~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       323 EAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            99999999999999999999999987764

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.97  E-value=9.2e-31  Score=307.83  Aligned_cols=265  Identities=19%  Similarity=0.331  Sum_probs=220.1

Q ss_pred             ccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCC---
Q 003463           76 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH---  145 (818)
Q Consensus        76 e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~---  145 (818)
                      .+||++|+.+++|.+++++|+.+|.|   .|+.|..+++++||+||.|.+.+.|.    .++...+.+..+++....   
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            58999999999999999999999986   68889889999999999999887554    233232444444443221   


Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      .......++|||+|||.++++++|+++|+.||.|.+|++    .++++|||||+|.+.++|++|++.++|..+.++.|.|
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v  161 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV  161 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEE
Confidence            112233568999999999999999999999999999874    4678999999999999999999999999999999999


Q ss_pred             cccCCCCCC-CCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCC
Q 003463          222 HFSIPKDNP-SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  296 (818)
Q Consensus       222 ~~a~pk~~~-~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG  296 (818)
                      ....++... ........+|||+||+.++|+++|+++|++||.|.++++    .+.++|||||+|.+.++|.+|++.|+|
T Consensus       162 ~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g  241 (562)
T TIGR01628       162 GRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG  241 (562)
T ss_pred             eccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            876655433 123334568999999999999999999999999999865    345688999999999999999999999


Q ss_pred             CccC----CceEEEEecCCCccc----------------------chhhhccchhccHHHHHHHHhhcCC
Q 003463          297 SDIA----GKRIKLEPSRPGGAR----------------------RNLMLQLNQELEQDESRILQHQVGS  340 (818)
Q Consensus       297 ~~i~----Gr~L~V~~a~~~~~r----------------------~~~~~ql~~~~~~~~l~~~f~~~Gs  340 (818)
                      ..+.    |+.|.|.+++.+.++                      ..++.++...+++++++.+|.+||.
T Consensus       242 ~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~  311 (562)
T TIGR01628       242 KKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGE  311 (562)
T ss_pred             cEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCC
Confidence            9999    999999988766544                      2467778889999999999999984

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=1e-29  Score=274.21  Aligned_cols=250  Identities=20%  Similarity=0.333  Sum_probs=207.9

Q ss_pred             ccCCCCCchhhhhhcCccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccC
Q 003463           58 IGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLL  130 (818)
Q Consensus        58 IgnLlPddeddl~~~v~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~  130 (818)
                      .+.-.|+ .|---...-+|+||++||.++.|++|+.+|...|.|   +|+.|+.++.++||+||+|.+++.|.    .++
T Consensus        68 ~ggPpP~-weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~ln  146 (506)
T KOG0117|consen   68 YGGPPPG-WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELN  146 (506)
T ss_pred             cCCCCCc-ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhh
Confidence            4444554 345555678999999999999999999999999987   69999999999999999999988655    444


Q ss_pred             ccccCCC-CccccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEE------eCCCcccEEEEEEccHHHH
Q 003463          131 HYSVPNG-AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLY------TACKHRGFVMISYYDIRAA  202 (818)
Q Consensus       131 ~~~l~n~-~~~~~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~-I~~v~------~~~ksrG~AFV~F~d~e~A  202 (818)
                      ++.+..+ .+.+     .....+++|||+|||.+.++++|.+.|++.++ |..|.      ...++||||||+|++...|
T Consensus       147 n~Eir~GK~igv-----c~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~A  221 (506)
T KOG0117|consen  147 NYEIRPGKLLGV-----CVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAA  221 (506)
T ss_pred             CccccCCCEeEE-----EEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhH
Confidence            4444322 1111     12346799999999999999999999999886 55554      2568999999999999999


Q ss_pred             HHHHHHhcC--cccccccccccccCCCCCCCCCCC-CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEE
Q 003463          203 RTAMRALQN--KPLRRRKLDIHFSIPKDNPSDKDL-NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFI  279 (818)
Q Consensus       203 ~~Al~~Lng--~~l~gr~L~V~~a~pk~~~~~~~~-~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFV  279 (818)
                      ..|.++|-.  ..+.|..+.|.|+.|+..+..+.. .-+.|||+||+.++|+|.|+++|++||.|.+|+..   +.||||
T Consensus       222 a~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~---rDYaFV  298 (506)
T KOG0117|consen  222 AMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP---RDYAFV  298 (506)
T ss_pred             HHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecc---cceeEE
Confidence            999988754  456799999999999887665433 33689999999999999999999999999999764   669999


Q ss_pred             EEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcccc
Q 003463          280 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  316 (818)
Q Consensus       280 eF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r~  316 (818)
                      .|.++++|.+|++.+||++|.|..|.|.+|+|..+++
T Consensus       299 Hf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  299 HFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             eecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            9999999999999999999999999999999976554

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.97  E-value=1.9e-29  Score=296.76  Aligned_cols=245  Identities=19%  Similarity=0.319  Sum_probs=198.9

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEE---EeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCC-
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGME---LEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH-  145 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i~---V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~-  145 (818)
                      ...++|++|+.++++.+++++|+.+|.|.   |..+ .++.++||+||.|.+.+.|.    .+++..+.+....+.... 
T Consensus        88 ~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628        88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccc
Confidence            46799999999999999999999999873   4333 46788999999999988665    233333333222221111 


Q ss_pred             -----CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccc-
Q 003463          146 -----PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR-  215 (818)
Q Consensus       146 -----~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~-  215 (818)
                           .......++|||+|||.++|+++|+++|+.||+|.++.+    .++++|||||+|.+.++|.+|++.|++..+. 
T Consensus       167 ~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~  246 (562)
T TIGR01628       167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL  246 (562)
T ss_pred             ccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecc
Confidence                 112234578999999999999999999999999999874    4678999999999999999999999999999 


Q ss_pred             ---cccccccccCCCCCCCC--------------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCC
Q 003463          216 ---RRKLDIHFSIPKDNPSD--------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKR  274 (818)
Q Consensus       216 ---gr~L~V~~a~pk~~~~~--------------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~sr  274 (818)
                         |+.+.|..+..+.....              ......+|||+||+.++|+++|+++|++||.|++|++    ++.++
T Consensus       247 ~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~  326 (562)
T TIGR01628       247 AKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSR  326 (562)
T ss_pred             cccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcC
Confidence               99999988765543210              1123457999999999999999999999999999976    46778


Q ss_pred             ceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcccchhh
Q 003463          275 HHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM  319 (818)
Q Consensus       275 G~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r~~~~  319 (818)
                      |||||+|.+.++|.+|+..|||+.+.|++|.|.++..+..++..+
T Consensus       327 g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~  371 (562)
T TIGR01628       327 GFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHL  371 (562)
T ss_pred             CeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHH
Confidence            999999999999999999999999999999999999887665433

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.96  E-value=4.6e-29  Score=288.50  Aligned_cols=235  Identities=21%  Similarity=0.320  Sum_probs=193.2

Q ss_pred             hcCccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccc----cCccccCCC-Ccccc
Q 003463           71 AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNG-AGTVA  142 (818)
Q Consensus        71 ~~v~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~----~~~~~l~n~-~~~~~  142 (818)
                      ....+++||++||.+++|++++++|..+|.|   .|+.| .++.++||+||.|.+.+.|..    ++++.+.++ ...+.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            4456899999999999999999999999976   57778 789999999999999886653    334433322 11111


Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEE------eCCCcccEEEEEEccHHHHHHHHHHhcC--cc
Q 003463          143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLY------TACKHRGFVMISYYDIRAARTAMRALQN--KP  213 (818)
Q Consensus       143 g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~-I~~v~------~~~ksrG~AFV~F~d~e~A~~Al~~Lng--~~  213 (818)
                           .....++|||+|||.++++++|.++|++++. |..+.      ..++++|||||+|.+.++|.+|++.|..  ..
T Consensus       134 -----~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~  208 (578)
T TIGR01648       134 -----ISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQ  208 (578)
T ss_pred             -----ccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceE
Confidence                 1234789999999999999999999999864 33332      1356899999999999999999998864  45


Q ss_pred             cccccccccccCCCCCCCCCC-CCccceeeecCCCCCCHHHHHHHhhcc--CCeEEEEecCCCCceEEEEEcCHHHHHHH
Q 003463          214 LRRRKLDIHFSIPKDNPSDKD-LNQGTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAA  290 (818)
Q Consensus       214 l~gr~L~V~~a~pk~~~~~~~-~~~~tL~V~NLp~~vteedL~~lFs~f--G~I~~vr~~g~srG~aFVeF~d~e~A~~A  290 (818)
                      +.|+.|.|.|+.++....... ...++|||+||+.++++++|+++|++|  |+|++|++.   ++||||+|.+.++|++|
T Consensus       209 l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kA  285 (578)
T TIGR01648       209 LWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKA  285 (578)
T ss_pred             ecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHH
Confidence            789999999998866443322 234689999999999999999999999  999999764   57999999999999999


Q ss_pred             HHHcCCCccCCceEEEEecCCCcc
Q 003463          291 LKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       291 i~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ++.|||.+|.|+.|+|.|+++...
T Consensus       286 i~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       286 MDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHHhCCCEECCEEEEEEEccCCCc
Confidence            999999999999999999988654

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=3.3e-29  Score=253.93  Aligned_cols=213  Identities=25%  Similarity=0.422  Sum_probs=177.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      .+..++|+|..||..+|+|||+.+|...|+|++|+     +++.+.||+||.|.+++||++|+..|+|.++..+.|+|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            34567899999999999999999999999999998     5889999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       224 a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ++|..    ..++..+|||++||+.+|..||+++|++||.|+..|     +++.+||.+||+|+.+.+|++||+.|||.+
T Consensus       118 ARPSs----~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  118 ARPSS----DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ccCCh----hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            99865    445677999999999999999999999999998765     478899999999999999999999999999


Q ss_pred             cCC--ceEEEEecCCCcccchhhhccchhccHHHHHHHHhhcCCCCCCCCCCCCccCCCCCCCCcccccc------CCCC
Q 003463          299 IAG--KRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTIS------KSPN  370 (818)
Q Consensus       299 i~G--r~L~V~~a~~~~~r~~~~~ql~~~~~~~~l~~~f~~~GsP~a~s~P~~~~~~~~p~~~~~~~~~~------~~~~  370 (818)
                      ..|  .+|.|+|+..+.++.....          +   ..-|++|.        +++++|++| +.|++.      +...
T Consensus       194 P~g~tepItVKFannPsq~t~~a~----------l---s~ly~sp~--------rr~~Gp~hh-~~~r~r~~~~~~~~~~  251 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNPSQKTNQAL----------L---SQLYQSPA--------RRYGGPMHH-QAQRFRLDNLLNPHAA  251 (360)
T ss_pred             CCCCCCCeEEEecCCcccccchhh----------h---HHhhcCcc--------ccCCCcccc-hhhhhccccccchhhh
Confidence            888  6899999987754432111          0   11233332        567889998 555542      2334


Q ss_pred             CCCCCCCcCCCCCCCcc
Q 003463          371 FRNMSPTTSNHMPGLAS  387 (818)
Q Consensus       371 ~~~~sP~~~~~~~g~~s  387 (818)
                      ..+|||++.+++.++++
T Consensus       252 ~~rfsP~~~d~m~~l~~  268 (360)
T KOG0145|consen  252 QARFSPMTIDGMSGLAG  268 (360)
T ss_pred             hccCCCccccccceeee
Confidence            55899998888877653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=6.6e-27  Score=258.96  Aligned_cols=159  Identities=21%  Similarity=0.406  Sum_probs=143.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +.++|||+|||.+++|++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            4789999999999999999999999999999874     56789999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      ++..    .....+|||+|||..+++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..+.
T Consensus        82 ~~~~----~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        82 PSSD----SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             cccc----ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            7543    234568999999999999999999999999988865     3457899999999999999999999999998


Q ss_pred             C--ceEEEEecCCCc
Q 003463          301 G--KRIKLEPSRPGG  313 (818)
Q Consensus       301 G--r~L~V~~a~~~~  313 (818)
                      |  .+|+|.++....
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            7  678899987654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.96  E-value=7.5e-28  Score=277.95  Aligned_cols=262  Identities=18%  Similarity=0.233  Sum_probs=201.3

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcEE-EeecCCCCCcccEEEEEecChhhccccC------ccccCCCCccccCCC--
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGME-LEGEPQESLSMSMSKISISDSASGNGLL------HYSVPNGAGTVAGEH--  145 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i~-V~~d~~t~~skG~a~v~f~~~~~a~~~~------~~~l~n~~~~~~g~~--  145 (818)
                      ..++|++||.+++|.+++++|+.+|.|. |..-    ..++++||.|.+.+.|..+.      ...+.+....+....  
T Consensus         3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~----~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMML----PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEE----CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            5689999999999999999999999984 2111    24689999999988665332      222333322221110  


Q ss_pred             ----CC-------CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCC-cccEEEEEEccHHHHHHHHHHhcCcc
Q 003463          146 ----PY-------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNKP  213 (818)
Q Consensus       146 ----~~-------~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~k-srG~AFV~F~d~e~A~~Al~~Lng~~  213 (818)
                          +.       ......+|||+||++.+|+++|+++|+.||+|.+|.+..+ .+++|||+|.+.++|++|++.|+|..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~  158 (481)
T TIGR01649        79 EIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGAD  158 (481)
T ss_pred             ccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCc
Confidence                00       0112247999999999999999999999999999985333 34799999999999999999999999


Q ss_pred             ccc--ccccccccCCCCCC-------C------------------------C----------------------------
Q 003463          214 LRR--RKLDIHFSIPKDNP-------S------------------------D----------------------------  232 (818)
Q Consensus       214 l~g--r~L~V~~a~pk~~~-------~------------------------~----------------------------  232 (818)
                      |.+  +.|+|.|+.+....       .                        .                            
T Consensus       159 i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  238 (481)
T TIGR01649       159 IYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGG  238 (481)
T ss_pred             ccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCccccc
Confidence            964  47777776542100       0                        0                            


Q ss_pred             --------------------------------CCCCccceeeecCCC-CCCHHHHHHHhhccCCeEEEEecCCCCceEEE
Q 003463          233 --------------------------------KDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFI  279 (818)
Q Consensus       233 --------------------------------~~~~~~tL~V~NLp~-~vteedL~~lFs~fG~I~~vr~~g~srG~aFV  279 (818)
                                                      ......+|||+||++ .+|+++|+++|+.||.|.+|++...++|+|||
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV  318 (481)
T TIGR01649       239 DRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALI  318 (481)
T ss_pred             ccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEE
Confidence                                            001235899999998 69999999999999999999987667899999


Q ss_pred             EEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc-----------------------------------------ccchh
Q 003463          280 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG-----------------------------------------ARRNL  318 (818)
Q Consensus       280 eF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~-----------------------------------------~r~~~  318 (818)
                      +|.+.++|.+|+..|||..|.|++|+|.+++...                                         .+..+
T Consensus       319 ~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~  398 (481)
T TIGR01649       319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLH  398 (481)
T ss_pred             EECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEE
Confidence            9999999999999999999999999999875421                                         01234


Q ss_pred             hhccchhccHHHHHHHHhhcCC
Q 003463          319 MLQLNQELEQDESRILQHQVGS  340 (818)
Q Consensus       319 ~~ql~~~~~~~~l~~~f~~~Gs  340 (818)
                      +.++...+++++++++|..+|.
T Consensus       399 v~NLp~~~tee~L~~lF~~~G~  420 (481)
T TIGR01649       399 LSNIPLSVSEEDLKELFAENGV  420 (481)
T ss_pred             EecCCCCCCHHHHHHHHHhcCC
Confidence            5677778889999999998883

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=7.3e-29  Score=251.40  Aligned_cols=246  Identities=19%  Similarity=0.305  Sum_probs=206.8

Q ss_pred             CCCcccccccCCCCCchhhhhhcCccccccccCCCCCChHHHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhcc--
Q 003463           50 LEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN--  127 (818)
Q Consensus        50 ~ee~~~~~IgnLlPddeddl~~~v~~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~--  127 (818)
                      .++.++..|.|+||..        |++..++.||.+++|+|.|++.+         |+.++++.||+||+|.+...|.  
T Consensus        37 t~~skTNLIvNYLPQ~--------MTqdE~rSLF~SiGeiEScKLvR---------DKitGqSLGYGFVNYv~p~DAe~A   99 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQN--------MTQDELRSLFGSIGEIESCKLVR---------DKITGQSLGYGFVNYVRPKDAEKA   99 (360)
T ss_pred             cCcccceeeeeecccc--------cCHHHHHHHhhcccceeeeeeee---------ccccccccccceeeecChHHHHHH
Confidence            5677899999999987        88888888888888888887765         6889999999999999876554  


Q ss_pred             --ccCccccCCCCccccCCCCCCC-CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccH
Q 003463          128 --GLLHYSVPNGAGTVAGEHPYGE-HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDI  199 (818)
Q Consensus       128 --~~~~~~l~n~~~~~~g~~~~~e-~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~  199 (818)
                        .+++.++.++.++++..+|..+ ....+|||.+||..+|..||..+|++||.|..-+     +++.+||.+||.|+..
T Consensus       100 intlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr  179 (360)
T KOG0145|consen  100 INTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKR  179 (360)
T ss_pred             HhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecch
Confidence              6777788888888888877644 4567999999999999999999999999986654     5788999999999999


Q ss_pred             HHHHHHHHHhcCccccc--ccccccccCCCCCCCC-------------C-------------------------------
Q 003463          200 RAARTAMRALQNKPLRR--RKLDIHFSIPKDNPSD-------------K-------------------------------  233 (818)
Q Consensus       200 e~A~~Al~~Lng~~l~g--r~L~V~~a~pk~~~~~-------------~-------------------------------  233 (818)
                      ++|++|++.|+|..-.|  .+|.|+|+........             .                               
T Consensus       180 ~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~  259 (360)
T KOG0145|consen  180 IEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMT  259 (360)
T ss_pred             hHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCcc
Confidence            99999999999988765  4688887643211000             0                               


Q ss_pred             ---------------CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHH
Q 003463          234 ---------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       234 ---------------~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~  293 (818)
                                     .....+|||.||.++.+|.-|+++|.+||.|..|++     +.+.|||+||.+.+.++|..||..
T Consensus       260 ~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~s  339 (360)
T KOG0145|consen  260 IDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS  339 (360)
T ss_pred             ccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHH
Confidence                           000138999999999999999999999999998865     467899999999999999999999


Q ss_pred             cCCCccCCceEEEEecCCC
Q 003463          294 LNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       294 LnG~~i~Gr~L~V~~a~~~  312 (818)
                      |||..+++|.|.|.|...+
T Consensus       340 LNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  340 LNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             hcCccccceEEEEEEecCC
Confidence            9999999999999997654

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.95  E-value=1.8e-26  Score=235.97  Aligned_cols=213  Identities=18%  Similarity=0.355  Sum_probs=174.1

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccccCccccCCCCccccCCCCCCC-C
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGE-H  150 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~~~~~~l~n~~~~~~g~~~~~e-~  150 (818)
                      +.++|++|...++|+-+..||...|.+   .|.+|..        +|.     ++..             .+...... .
T Consensus         7 rtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~--------~v~-----wa~~-------------p~nQsk~t~~   60 (321)
T KOG0148|consen    7 RTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL--------KVN-----WATA-------------PGNQSKPTSN   60 (321)
T ss_pred             ceEEeeccChhhHHHHHHHHHHhccccccceeehhhh--------ccc-----cccC-------------cccCCCCccc
Confidence            568889999999999999999998877   3555510        010     0000             01111111 1


Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .--.+||+.|...++-|+|++.|.+||+|.++++     ++|+|||+||.|.+.++|++||..|+|..|.+|.|+-.|+.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            1246999999999999999999999999988873     78999999999999999999999999999999999999997


Q ss_pred             CCCCCCC------------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHH
Q 003463          226 PKDNPSD------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       226 pk~~~~~------------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~  293 (818)
                      .|.....            .....++|||+|++.-+||++|++.|++||.|.+||+.+ -+||+||+|++.|+|.+||..
T Consensus       141 RKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk-~qGYaFVrF~tkEaAahAIv~  219 (321)
T KOG0148|consen  141 RKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFK-DQGYAFVRFETKEAAAHAIVQ  219 (321)
T ss_pred             cCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEec-ccceEEEEecchhhHHHHHHH
Confidence            6642211            123457999999999999999999999999999999974 479999999999999999999


Q ss_pred             cCCCccCCceEEEEecCCCcc
Q 003463          294 LNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       294 LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      +|+.+|.|..+++.|.+....
T Consensus       220 mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  220 MNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             hcCceeCceEEEEeccccCCC
Confidence            999999999999999987654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.94  E-value=1.6e-26  Score=255.09  Aligned_cols=163  Identities=23%  Similarity=0.419  Sum_probs=145.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      .....++|||+|||+++||++|+++|+.||+|++|++     +++++|||||+|.+.++|++|++.|++..|.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            3456789999999999999999999999999999874     56789999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCC
Q 003463          223 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS  297 (818)
Q Consensus       223 ~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~  297 (818)
                      ++.+...    .....+|||.|||.++|+++|+++|++||.|+.+++     +++++++|||+|.+.++|++||+.||+.
T Consensus       183 ~a~p~~~----~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  258 (346)
T TIGR01659       183 YARPGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV  258 (346)
T ss_pred             ccccccc----ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            9876432    234568999999999999999999999999998865     4566899999999999999999999999


Q ss_pred             ccCC--ceEEEEecCCCcc
Q 003463          298 DIAG--KRIKLEPSRPGGA  314 (818)
Q Consensus       298 ~i~G--r~L~V~~a~~~~~  314 (818)
                      .+.|  ++|+|.+++....
T Consensus       259 ~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       259 IPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             ccCCCceeEEEEECCcccc
Confidence            8876  7899999886543

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=4.6e-26  Score=263.13  Aligned_cols=162  Identities=25%  Similarity=0.335  Sum_probs=140.1

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          151 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       151 ~srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      ++++|||+|||. .+|+++|+++|+.||.|..|++....+|||||+|.+.++|++|++.|+|..|.|++|+|.++..+..
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~  353 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNV  353 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccc
Confidence            567999999998 6999999999999999999997655689999999999999999999999999999999998754321


Q ss_pred             CCC------------C---------------------CCCccceeeecCCCCCCHHHHHHHhhccCC--eEEEEecCC--
Q 003463          230 PSD------------K---------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGE--VKEIRETPH--  272 (818)
Q Consensus       230 ~~~------------~---------------------~~~~~tL~V~NLp~~vteedL~~lFs~fG~--I~~vr~~g~--  272 (818)
                      ...            +                     .....+|||+|||.++++++|+++|+.||.  |+.|++...  
T Consensus       354 ~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~  433 (481)
T TIGR01649       354 QPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDN  433 (481)
T ss_pred             cCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCC
Confidence            000            0                     012358999999999999999999999998  888877433  


Q ss_pred             -CCceEEEEEcCHHHHHHHHHHcCCCccCCce------EEEEecCCC
Q 003463          273 -KRHHKFIEFYDVRAAEAALKSLNRSDIAGKR------IKLEPSRPG  312 (818)
Q Consensus       273 -srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~------L~V~~a~~~  312 (818)
                       ++++|||+|.+.++|.+||..|||..|.|+.      |+|.|++++
T Consensus       434 ~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       434 ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence             3789999999999999999999999999985      999999864

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.94  E-value=1.3e-25  Score=257.54  Aligned_cols=238  Identities=21%  Similarity=0.286  Sum_probs=189.1

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCccccC----
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVAG----  143 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~~~~g----  143 (818)
                      ...+||++||..+++.++.++|..+|.|   .|..|..++.++||+||.|.+.+.|.   .+.+..+.+..+.+..    
T Consensus        89 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622        89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchh
Confidence            4679999999999999999999999987   57778889999999999999877554   3333333333221110    


Q ss_pred             ---------CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHh
Q 003463          144 ---------EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL  209 (818)
Q Consensus       144 ---------~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~L  209 (818)
                               .........++|||+|||.++++++|+++|+.||.|..|.+     +++++|||||+|.+.++|.+|++.|
T Consensus       169 ~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l  248 (457)
T TIGR01622       169 KNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM  248 (457)
T ss_pred             hhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhc
Confidence                     00011123689999999999999999999999999999874     3578999999999999999999999


Q ss_pred             cCcccccccccccccCCCCCCC----------------------------------C-----------------------
Q 003463          210 QNKPLRRRKLDIHFSIPKDNPS----------------------------------D-----------------------  232 (818)
Q Consensus       210 ng~~l~gr~L~V~~a~pk~~~~----------------------------------~-----------------------  232 (818)
                      +|..|.|++|.|.|+.......                                  .                       
T Consensus       249 ~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (457)
T TIGR01622       249 NGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD  328 (457)
T ss_pred             CCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccc
Confidence            9999999999999953110000                                  0                       


Q ss_pred             -----------------------------CCCCccceeeecCCCCCC----------HHHHHHHhhccCCeEEEEec-CC
Q 003463          233 -----------------------------KDLNQGTLVVFNLDPSVS----------NEDLRQIFGAYGEVKEIRET-PH  272 (818)
Q Consensus       233 -----------------------------~~~~~~tL~V~NLp~~vt----------eedL~~lFs~fG~I~~vr~~-g~  272 (818)
                                                   ......+|+|.||....+          .+||++.|++||.|+.|.+. +.
T Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~  408 (457)
T TIGR01622       329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKN  408 (457)
T ss_pred             ccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCC
Confidence                                         001234688888855443          37899999999999999875 67


Q ss_pred             CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          273 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       273 srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..|++||+|.+.++|.+|++.|||..++|+.|.|.|...
T Consensus       409 ~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       409 SAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             CceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            789999999999999999999999999999999999754

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.94  E-value=2.4e-25  Score=258.58  Aligned_cols=238  Identities=16%  Similarity=0.228  Sum_probs=178.9

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---------EEeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCccc
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---------ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTV  141 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---------~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~~~  141 (818)
                      ...+||++||..+++.+|.++|..++..         .+..+......+||+||.|.+.+.|.   .+.+..+.+...++
T Consensus       175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v  254 (509)
T TIGR01642       175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKI  254 (509)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEe
Confidence            4679999999999999999999874110         01122234566899999999887554   23332222222111


Q ss_pred             cCCC------------------------------CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CC
Q 003463          142 AGEH------------------------------PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----AC  186 (818)
Q Consensus       142 ~g~~------------------------------~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~  186 (818)
                      ....                              .......++|||+|||..+++++|+++|+.||.|..+.+     ++
T Consensus       255 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g  334 (509)
T TIGR01642       255 RRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATG  334 (509)
T ss_pred             cCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCC
Confidence            1000                              001234579999999999999999999999999998763     57


Q ss_pred             CcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCC------------------------CCCCccceee
Q 003463          187 KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD------------------------KDLNQGTLVV  242 (818)
Q Consensus       187 ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~------------------------~~~~~~tL~V  242 (818)
                      +++|||||+|.+.++|+.|++.|+|..|.|+.|.|.++........                        ......+|+|
T Consensus       335 ~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l  414 (509)
T TIGR01642       335 LSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQL  414 (509)
T ss_pred             CcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceEEEe
Confidence            7899999999999999999999999999999999998754321110                        0113457899


Q ss_pred             ecCCCC--C--------CHHHHHHHhhccCCeEEEEecC--------CCCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          243 FNLDPS--V--------SNEDLRQIFGAYGEVKEIRETP--------HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       243 ~NLp~~--v--------teedL~~lFs~fG~I~~vr~~g--------~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                      .|+...  +        ..++|+++|++||.|+.|++..        ...|+|||+|.+.++|++|+.+|||..|.|+.|
T Consensus       415 ~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v  494 (509)
T TIGR01642       415 TNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVV  494 (509)
T ss_pred             ccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            998632  1        2368999999999999998632        236899999999999999999999999999999


Q ss_pred             EEEecCC
Q 003463          305 KLEPSRP  311 (818)
Q Consensus       305 ~V~~a~~  311 (818)
                      .|.|...
T Consensus       495 ~~~~~~~  501 (509)
T TIGR01642       495 VAAFYGE  501 (509)
T ss_pred             EEEEeCH
Confidence            9999754

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.92  E-value=2.4e-24  Score=249.72  Aligned_cols=163  Identities=20%  Similarity=0.402  Sum_probs=143.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            4589999999999999999999999999999984     67899999999999999999999999999999999998654


Q ss_pred             CCCCCC-------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHH
Q 003463          226 PKDNPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       226 pk~~~~-------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~  293 (818)
                      ......       .......+|||+||++++++++|+++|+.||.|+++++     ++.++|||||+|.+.++|.+||..
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            221110       11123468999999999999999999999999999976     345789999999999999999999


Q ss_pred             cCCCccCCceEEEEecCCCc
Q 003463          294 LNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       294 LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ||+.+++|+.|+|.++.++.
T Consensus       266 mNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             hCCCeeCCeEEEEEecCCCc
Confidence            99999999999999988654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=9.7e-24  Score=227.18  Aligned_cols=163  Identities=23%  Similarity=0.442  Sum_probs=143.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcc-ccc--cccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKP-LRR--RKLDIH  222 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~-l~g--r~L~V~  222 (818)
                      ..-+|||+-||..++|+||+++|++||.|.+|.     .++.++|||||.|++.++|.+|+.+|++.. |.|  .+|.|+
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            456899999999999999999999999999886     477899999999999999999999998855 444  688999


Q ss_pred             ccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCC-
Q 003463          223 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRS-  297 (818)
Q Consensus       223 ~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~-  297 (818)
                      |+....++.   ..+.+|||+-|++.+||.|++++|++||.|++|++    .+.+||||||+|.+.+.|..||++|||. 
T Consensus       113 ~Ad~E~er~---~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  113 YADGERERI---VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             ccchhhhcc---ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccce
Confidence            987654332   44678999999999999999999999999999965    5678999999999999999999999997 


Q ss_pred             ccCC--ceEEEEecCCCcccc
Q 003463          298 DIAG--KRIKLEPSRPGGARR  316 (818)
Q Consensus       298 ~i~G--r~L~V~~a~~~~~r~  316 (818)
                      .+.|  .+|.|+|+.+++.|.
T Consensus       190 tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  190 TMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             eeccCCCceEEEecccCCCch
Confidence            6666  689999999887664

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=3e-23  Score=228.43  Aligned_cols=240  Identities=19%  Similarity=0.293  Sum_probs=189.3

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----cc-----CccccCCCCc---
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GL-----LHYSVPNGAG---  139 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~-----~~~~l~n~~~---  139 (818)
                      ..+||++||.+++..++.++|+..|.|   +|..+..++..+||+||+|+-.+...    ..     .+..+.-...   
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            469999999999999999999999987   68888889999999999999554322    11     1111111100   


Q ss_pred             -cc----cC-----CCCC---------CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEE
Q 003463          140 -TV----AG-----EHPY---------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISY  196 (818)
Q Consensus       140 -~~----~g-----~~~~---------~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F  196 (818)
                       +.    .+     +.+.         ...+.-+|+|+|||+.+.+.+|+.+|+.||.|..|.+    .++-.|||||+|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence             00    00     1111         1223568999999999999999999999999999985    455679999999


Q ss_pred             ccHHHHHHHHHHhcCcccccccccccccCCCCCCCC-----------------------------------------C--
Q 003463          197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-----------------------------------------K--  233 (818)
Q Consensus       197 ~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~-----------------------------------------~--  233 (818)
                      .+..+|.+|++.+|+..|.||+|-|.|+.++..-..                                         +  
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~  245 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEET  245 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccc
Confidence            999999999999999999999999999865431000                                         0  


Q ss_pred             CC-------------------------------------------CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-
Q 003463          234 DL-------------------------------------------NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-  269 (818)
Q Consensus       234 ~~-------------------------------------------~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-  269 (818)
                      +.                                           ...+|||+|||+++|+++|.+.|++||.|..+.+ 
T Consensus       246 D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV  325 (678)
T KOG0127|consen  246 DGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV  325 (678)
T ss_pred             cccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEE
Confidence            00                                           0048999999999999999999999999998753 


Q ss_pred             ----cCCCCceEEEEEcCHHHHHHHHHHc-----CC-CccCCceEEEEecCCCcc
Q 003463          270 ----TPHKRHHKFIEFYDVRAAEAALKSL-----NR-SDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       270 ----~g~srG~aFVeF~d~e~A~~Ai~~L-----nG-~~i~Gr~L~V~~a~~~~~  314 (818)
                          ++.++|.|||.|.+..+|.+||...     .| ..+.||.|+|..+-++..
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHH
Confidence                7889999999999999999999977     23 678899999999876553

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=1.1e-23  Score=226.78  Aligned_cols=241  Identities=19%  Similarity=0.330  Sum_probs=193.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccc----cCccccCCC---CccccC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNG---AGTVAG  143 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~----~~~~~l~n~---~~~~~g  143 (818)
                      .-++||+.+|+..+|.|++.+|..+|.|   -|.+|+.+++++||+||.|.+.+.|.+    +.+.+...+   +..+..
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            3569999999999999999999999987   478899999999999999998776542    222222222   222222


Q ss_pred             CCCCCC--CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcc-ccc
Q 003463          144 EHPYGE--HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKP-LRR  216 (818)
Q Consensus       144 ~~~~~e--~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~-l~g  216 (818)
                      .....+  ...++|||+-|+..+||.|++++|++||.|++|++    .+.+||||||.|.+.|.|..||+.||+.. ++|
T Consensus       114 Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeG  193 (510)
T KOG0144|consen  114 ADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEG  193 (510)
T ss_pred             cchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeecc
Confidence            211112  23689999999999999999999999999999984    56799999999999999999999999954 554


Q ss_pred             --ccccccccCCCCCCCCCCC-----------------------------------------------------------
Q 003463          217 --RKLDIHFSIPKDNPSDKDL-----------------------------------------------------------  235 (818)
Q Consensus       217 --r~L~V~~a~pk~~~~~~~~-----------------------------------------------------------  235 (818)
                        .+|.|+|+++++.+..+..                                                           
T Consensus       194 cs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~  273 (510)
T KOG0144|consen  194 CSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQ  273 (510)
T ss_pred             CCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhH
Confidence              5788888776543110000                                                           


Q ss_pred             --------------------------------------------------------------------------------
Q 003463          236 --------------------------------------------------------------------------------  235 (818)
Q Consensus       236 --------------------------------------------------------------------------------  235 (818)
                                                                                                      
T Consensus       274 ~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~  353 (510)
T KOG0144|consen  274 LQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAG  353 (510)
T ss_pred             HHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhccccccccc
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------------------CccceeeecCC
Q 003463          236 ---------------------------------------------------------------------NQGTLVVFNLD  246 (818)
Q Consensus       236 ---------------------------------------------------------------------~~~tL~V~NLp  246 (818)
                                                                                           ...+|||.+||
T Consensus       354 a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlP  433 (510)
T KOG0144|consen  354 AGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLP  433 (510)
T ss_pred             ccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCc
Confidence                                                                                 00279999999


Q ss_pred             CCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          247 PSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       247 ~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      .+.-+.||...|.+||.|++.+     .++-++.|+||.|++..+|.+||..|||..|+.++++|...+.+..
T Consensus       434 qefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  434 QEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             hhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            9999999999999999998875     3667899999999999999999999999999999999999876553

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.89  E-value=8.1e-23  Score=234.47  Aligned_cols=163  Identities=25%  Similarity=0.450  Sum_probs=142.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++||. |+|..+.|++|.|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~  163 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ  163 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEe
Confidence            3456789999999999999999999999999999884     56789999999999999999997 89999999999998


Q ss_pred             ccCCCCCCCC--------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHH
Q 003463          223 FSIPKDNPSD--------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEA  289 (818)
Q Consensus       223 ~a~pk~~~~~--------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~  289 (818)
                      ++........        ......+|||+|||..+|+++|+++|++||.|..|++.     +.++|||||+|.+.++|.+
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~  243 (457)
T TIGR01622       164 SSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKE  243 (457)
T ss_pred             ecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            8654322111        11224789999999999999999999999999998753     4678999999999999999


Q ss_pred             HHHHcCCCccCCceEEEEecCC
Q 003463          290 ALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       290 Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      |+..|||..|.|+.|+|.|+..
T Consensus       244 A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       244 ALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHhcCCcEECCEEEEEEEccC
Confidence            9999999999999999999873

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.89  E-value=1e-21  Score=228.08  Aligned_cols=153  Identities=12%  Similarity=0.228  Sum_probs=126.0

Q ss_pred             CccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCC
Q 003463           73 IMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH  145 (818)
Q Consensus        73 v~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~  145 (818)
                      .+.++||++|+.+++|.+++++|..+|.|   .+.+|..+++++||+||.|.+.+.+.    .+++..+.+...++....
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46789999999999999999999999987   57788899999999999999987654    344444444433332111


Q ss_pred             C------------CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHH
Q 003463          146 P------------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRA  208 (818)
Q Consensus       146 ~------------~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~  208 (818)
                      .            ......++|||+|||.++++++|+++|+.||.|.++++     +++++|||||+|.+.++|.+|++.
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            0            11123579999999999999999999999999999874     467899999999999999999999


Q ss_pred             hcCcccccccccccccC
Q 003463          209 LQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       209 Lng~~l~gr~L~V~~a~  225 (818)
                      ||+..|.|+.|+|.++.
T Consensus       266 mNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             hCCCeeCCeEEEEEecC
Confidence            99999999999987654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.88  E-value=3.9e-22  Score=231.16  Aligned_cols=178  Identities=22%  Similarity=0.321  Sum_probs=153.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccc-cccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~-gr~L~V~~a~  225 (818)
                      ..++|||+|||.+++|++|+++|++||.|.+|++    +++++|||||+|.+.++|++||+.|++..|. ++.|.|..+.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            3589999999999999999999999999999874    5789999999999999999999999999986 7777776553


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCC-eEEEEe------cCCCCceEEEEEcCHHHHHHHHHHcCC--
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNR--  296 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~-I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~LnG--  296 (818)
                                ..++|||+|||.++++++|.+.|++++. |+++.+      ..+++|||||+|.+.++|.+|++.|+.  
T Consensus       137 ----------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gk  206 (578)
T TIGR01648       137 ----------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGR  206 (578)
T ss_pred             ----------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccc
Confidence                      2468999999999999999999999863 333322      245689999999999999999998864  


Q ss_pred             CccCCceEEEEecCCCcc---------cchhhhccchhccHHHHHHHHhhc
Q 003463          297 SDIAGKRIKLEPSRPGGA---------RRNLMLQLNQELEQDESRILQHQV  338 (818)
Q Consensus       297 ~~i~Gr~L~V~~a~~~~~---------r~~~~~ql~~~~~~~~l~~~f~~~  338 (818)
                      ..+.|+.|.|+|+.+...         +..++.++..++++++|+.+|.+|
T Consensus       207 i~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f  257 (578)
T TIGR01648       207 IQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF  257 (578)
T ss_pred             eEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhc
Confidence            367899999999987542         346889999999999999999999

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.88  E-value=7.7e-22  Score=219.25  Aligned_cols=229  Identities=15%  Similarity=0.310  Sum_probs=189.8

Q ss_pred             ccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCCCC
Q 003463           76 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  148 (818)
Q Consensus        76 e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~~~  148 (818)
                      .++|+   .+++|..++++|+..|.+   +|+.|. +  +.||++++|.+...|.    .++...+.+..+++.+...  
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r--   74 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR--   74 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc--
Confidence            35666   889999999999999976   799998 6  9999999999876543    4444444555666654422  


Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                        ..+.|||.||+++++.++|.++|+.||+|.+|++   ..-++|| ||+|.++++|++|++.++|..+.+++|.|....
T Consensus        75 --d~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   75 --DPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             --CCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence              2233999999999999999999999999999994   2238999 999999999999999999999999999998876


Q ss_pred             CCCCCCCCC----CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCC
Q 003463          226 PKDNPSDKD----LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRS  297 (818)
Q Consensus       226 pk~~~~~~~----~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~  297 (818)
                      .+..+....    ..-..++|.|++.++++++|..+|..||.|..+.+    .+.+++|+||+|.+.++|..|++.|++.
T Consensus       152 ~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~  231 (369)
T KOG0123|consen  152 RKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGK  231 (369)
T ss_pred             chhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCC
Confidence            655433222    22358999999999999999999999999999865    4557899999999999999999999999


Q ss_pred             ccCCceEEEEecCCCccc
Q 003463          298 DIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       298 ~i~Gr~L~V~~a~~~~~r  315 (818)
                      .+.++.+.|..+..+.++
T Consensus       232 ~~~~~~~~V~~aqkk~e~  249 (369)
T KOG0123|consen  232 IFGDKELYVGRAQKKSER  249 (369)
T ss_pred             cCCccceeecccccchhh
Confidence            999999999888775443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.87  E-value=1.9e-21  Score=225.98  Aligned_cols=163  Identities=17%  Similarity=0.304  Sum_probs=135.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcC------------CCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQY------------GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~f------------G~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                      .....++|||+|||+++|+++|+++|..+            +.|..+. .++.+|||||+|.+.++|..||+ |+|..|.
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~-~~~~kg~afVeF~~~e~A~~Al~-l~g~~~~  248 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN-INKEKNFAFLEFRTVEEATFAMA-LDSIIYS  248 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE-ECCCCCEEEEEeCCHHHHhhhhc-CCCeEee
Confidence            34567899999999999999999999975            3445444 46789999999999999999995 9999999


Q ss_pred             cccccccccCCCCC------------C-------------CCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-
Q 003463          216 RRKLDIHFSIPKDN------------P-------------SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-  269 (818)
Q Consensus       216 gr~L~V~~a~pk~~------------~-------------~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-  269 (818)
                      |+.|+|........            .             ........+|||+|||..+|+++|+++|+.||.|..+.+ 
T Consensus       249 g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~  328 (509)
T TIGR01642       249 NVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLI  328 (509)
T ss_pred             CceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE
Confidence            99999864321110            0             000112358999999999999999999999999998864 


Q ss_pred             ----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          270 ----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       270 ----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                          ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
T Consensus       329 ~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       329 KDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             ecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence                4668999999999999999999999999999999999998643

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.87  E-value=2e-21  Score=210.41  Aligned_cols=180  Identities=22%  Similarity=0.353  Sum_probs=158.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccc-ccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~-gr~L~V~~a  224 (818)
                      ..+-|||+.||.++.|+||.-+|++.|+|-+++     .++.+||||||.|.+.++|++|++.||+.+|+ |+.|.|..+
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            458999999999999999999999999999998     36889999999999999999999999999996 899999877


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCC-eEEEEe------cCCCCceEEEEEcCHHHHHHHHHHcCCC
Q 003463          225 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRS  297 (818)
Q Consensus       225 ~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~-I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~LnG~  297 (818)
                      .          .+++|||+|||++.++++|++.|++.++ |.+|.+      ..++||||||+|++..+|..|.++|-..
T Consensus       162 v----------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g  231 (506)
T KOG0117|consen  162 V----------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPG  231 (506)
T ss_pred             e----------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCC
Confidence            5          3568999999999999999999999863 444432      4567999999999999999999888543


Q ss_pred             --ccCCceEEEEecCCCcc---------cchhhhccchhccHHHHHHHHhhcCC
Q 003463          298 --DIAGKRIKLEPSRPGGA---------RRNLMLQLNQELEQDESRILQHQVGS  340 (818)
Q Consensus       298 --~i~Gr~L~V~~a~~~~~---------r~~~~~ql~~~~~~~~l~~~f~~~Gs  340 (818)
                        .+-|..+.|+||.|...         +..|++++...++++.|...|.++|.
T Consensus       232 ~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~  285 (506)
T KOG0117|consen  232 KIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGK  285 (506)
T ss_pred             ceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccc
Confidence              66799999999998653         34689999999999999999999983

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.85  E-value=5.6e-21  Score=186.31  Aligned_cols=163  Identities=24%  Similarity=0.338  Sum_probs=143.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....||||+||+..++++-|+++|-+.|+|..++     ++.+.+|||||+|.++|+|+-|++.|+...|.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            3457999999999999999999999999999997     46679999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEE------EecCCCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          225 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       225 ~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v------r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ...   ........+|||+||++.+++..|.+.|+.||.+...      ..++.+++++||.|.+.+.+.+|+..+||+.
T Consensus        87 s~~---~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~  163 (203)
T KOG0131|consen   87 SAH---QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             ccc---cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence            621   1222234689999999999999999999999988763      2467889999999999999999999999999


Q ss_pred             cCCceEEEEecCCCccc
Q 003463          299 IAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       299 i~Gr~L~V~~a~~~~~r  315 (818)
                      +..++|+|.++..+..+
T Consensus       164 l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  164 LCNRPITVSYAFKKDTK  180 (203)
T ss_pred             hcCCceEEEEEEecCCC
Confidence            99999999999776543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.83  E-value=9.2e-21  Score=195.90  Aligned_cols=148  Identities=28%  Similarity=0.462  Sum_probs=137.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD  232 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~  232 (818)
                      -+|||+|||..+++.+|+.+|++||+|.+|.+   -|.||||..++...|+.|++.|++-.|.|..|.|+-++.|.    
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDI---vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs----   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDI---VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS----   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeee---ecccceEEeecccccHHHHhhcccceecceEEEEEeccccC----
Confidence            36999999999999999999999999999986   46799999999999999999999999999999999887653    


Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                        ....+|+|+||.+.++.+||+..|++||.|+++++.   ++|+||.|+-.++|..|++.|++.++.|++++|..+..+
T Consensus        76 --k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv---kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   76 --KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV---KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             --CCccccccCCCCccccCHHHhhhhcccCCceeeeee---cceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence              245689999999999999999999999999999986   689999999999999999999999999999999998654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.81  E-value=1.4e-19  Score=199.68  Aligned_cols=161  Identities=22%  Similarity=0.365  Sum_probs=142.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      .||||++||++++.++|.++|+.+|+|..+.+     ...++||+||+|.-.+++++|++.+.+..+.|+.|.|.++.++
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            79999999999999999999999999999873     3468999999999999999999999999999999999998765


Q ss_pred             CCCCCC----------------------CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEE
Q 003463          228 DNPSDK----------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEF  281 (818)
Q Consensus       228 ~~~~~~----------------------~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF  281 (818)
                      ......                      +.....|.|+|||+.+...+|+.+|+.||.|.+|.+.    ++-+|||||+|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence            432210                      0113589999999999999999999999999999763    34469999999


Q ss_pred             cCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          282 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       282 ~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      .+..+|.+|++.+||.+|.||+|-|.||-++.
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            99999999999999999999999999998765

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=2.3e-19  Score=199.48  Aligned_cols=237  Identities=24%  Similarity=0.392  Sum_probs=190.3

Q ss_pred             cccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcccc----CccccCCCCccc-------c
Q 003463           77 FDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL----LHYSVPNGAGTV-------A  142 (818)
Q Consensus        77 ~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~~----~~~~l~n~~~~~-------~  142 (818)
                      ++|.+|+.+++..++.|+|+.+|.|   .|..|..  -++|+ ||.|.+.+.|..+    ++..+.+...-+       .
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~--g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN--GSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC--Cceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            9999999999999999999999998   5665543  29999 9999998876532    222222221111       1


Q ss_pred             CCCCCCC--CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccc
Q 003463          143 GEHPYGE--HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR  216 (818)
Q Consensus       143 g~~~~~e--~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g  216 (818)
                      ...+..+  ..-+.++|.+++.++++++|..+|..||.|.++.+    .+++++|+||.|.+.++|..|++.|++..+.+
T Consensus       156 r~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~  235 (369)
T KOG0123|consen  156 REAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGD  235 (369)
T ss_pred             hcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCc
Confidence            1111111  23468999999999999999999999999999873    56789999999999999999999999999999


Q ss_pred             ccccccccCCCCCCC--------------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEE
Q 003463          217 RKLDIHFSIPKDNPS--------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKF  278 (818)
Q Consensus       217 r~L~V~~a~pk~~~~--------------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aF  278 (818)
                      ..+.|..+..+....              .......+|||.||+..++.+.|+++|+.||.|..+++    .+.++|++|
T Consensus       236 ~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gf  315 (369)
T KOG0123|consen  236 KELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGF  315 (369)
T ss_pred             cceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccceEE
Confidence            998888765532111              11234468999999999999999999999999999865    467899999


Q ss_pred             EEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcccc
Q 003463          279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  316 (818)
Q Consensus       279 VeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r~  316 (818)
                      |+|.+.++|.+|+..+|+..+.++.|.|.++.....++
T Consensus       316 V~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~  353 (369)
T KOG0123|consen  316 VEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRR  353 (369)
T ss_pred             EEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccch
Confidence            99999999999999999999999999999988555444

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.80  E-value=2.3e-19  Score=204.10  Aligned_cols=161  Identities=25%  Similarity=0.456  Sum_probs=139.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCC--------CcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC--------KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~--------ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +|||+||++++|.++|..+|...|.|.++.+..        .+.|||||+|.+.++|+.|++.|+|..|+|+.|.|+++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            399999999999999999999999999996421        245999999999999999999999999999999999987


Q ss_pred             CCCC-----CCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCC-----CCceEEEEEcCHHHHHHHHHHcC
Q 003463          226 PKDN-----PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-----KRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       226 pk~~-----~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~-----srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      .+..     ..........|.|+|||+..+..+++++|..||.|++|++..+     .+|||||+|-+.++|.+|+.+|.
T Consensus       597 ~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~  676 (725)
T KOG0110|consen  597 NKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALG  676 (725)
T ss_pred             CccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhc
Confidence            2111     0111112358999999999999999999999999999988543     48899999999999999999999


Q ss_pred             CCccCCceEEEEecCCCcc
Q 003463          296 RSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       296 G~~i~Gr~L~V~~a~~~~~  314 (818)
                      .+.+.||+|.++|++....
T Consensus       677 STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  677 STHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             ccceechhhheehhccchH
Confidence            9999999999999987653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=2e-18  Score=191.02  Aligned_cols=154  Identities=20%  Similarity=0.310  Sum_probs=128.2

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  146 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~  146 (818)
                      .+++||++||.+++|.+|+++|+.+|.|   .|..|..+++++||+||.|.+.+.|.    .++...+.+..+++....+
T Consensus       107 ~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p  186 (346)
T TIGR01659       107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP  186 (346)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence            5789999999999999999999999987   57778889999999999999887554    3455555555555544333


Q ss_pred             C-CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccc--cc
Q 003463          147 Y-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RK  218 (818)
Q Consensus       147 ~-~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~  218 (818)
                      . .....++|||+|||.++|+++|+++|++||+|+.|++     +++.+|||||+|.+.++|++||+.|++..+.+  ++
T Consensus       187 ~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~  266 (346)
T TIGR01659       187 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQP  266 (346)
T ss_pred             cccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCcee
Confidence            2 2234678999999999999999999999999998873     56788999999999999999999999998876  68


Q ss_pred             ccccccCCC
Q 003463          219 LDIHFSIPK  227 (818)
Q Consensus       219 L~V~~a~pk  227 (818)
                      |.|.++...
T Consensus       267 l~V~~a~~~  275 (346)
T TIGR01659       267 LTVRLAEEH  275 (346)
T ss_pred             EEEEECCcc
Confidence            888887653

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=3.1e-18  Score=181.03  Aligned_cols=157  Identities=22%  Similarity=0.465  Sum_probs=138.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      -++|||+.|.+.+.|+.|+..|..||+|++|.     .+++++|||||+|+-.|.|+-|++.+||..+.||.|+|..  |
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr--P  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR--P  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC--C
Confidence            47899999999999999999999999999998     5889999999999999999999999999999999999984  3


Q ss_pred             CCCCCC---------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHH
Q 003463          227 KDNPSD---------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALK  292 (818)
Q Consensus       227 k~~~~~---------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~  292 (818)
                      ...+..         +...-.+|||..+.++++++||+.+|+.||+|+.|.+     ....+||+||||.+..+-.+||.
T Consensus       191 sNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAia  270 (544)
T KOG0124|consen  191 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  270 (544)
T ss_pred             CCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhh
Confidence            222211         1122358999999999999999999999999999976     23468999999999999999999


Q ss_pred             HcCCCccCCceEEEEecC
Q 003463          293 SLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       293 ~LnG~~i~Gr~L~V~~a~  310 (818)
                      .||=..++|..|+|..+-
T Consensus       271 sMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  271 SMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hcchhhcccceEeccccc
Confidence            999999999999997654

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.74  E-value=1e-17  Score=172.14  Aligned_cols=161  Identities=24%  Similarity=0.371  Sum_probs=130.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ++..|||||+||..+|||+-|..||.+.|.|..+++...                              .|+|.++....
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~------------------------------e~~v~wa~~p~   52 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD------------------------------ELKVNWATAPG   52 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh------------------------------hhccccccCcc
Confidence            345699999999999999999999999999998874221                              45666655443


Q ss_pred             CCCCCCCC-ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          229 NPSDKDLN-QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       229 ~~~~~~~~-~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      ..+....+ .--++|+.|.+.++.++|++.|.+||+|.++|+     ++++|||+||.|.+.++|++||..|||..|++|
T Consensus        53 nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen   53 NQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             cCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccc
Confidence            33333322 346899999999999999999999999998875     678999999999999999999999999999999


Q ss_pred             eEEEEecCCCccc--------------------chhhhccchhccHHHHHHHHhhcC
Q 003463          303 RIKLEPSRPGGAR--------------------RNLMLQLNQELEQDESRILQHQVG  339 (818)
Q Consensus       303 ~L~V~~a~~~~~r--------------------~~~~~ql~~~~~~~~l~~~f~~~G  339 (818)
                      .|+-.||..|...                    ..|+...+..++++.++..|.+||
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG  189 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFG  189 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCC
Confidence            9999999665422                    235556666678888888888777

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.73  E-value=1.6e-17  Score=184.89  Aligned_cols=237  Identities=19%  Similarity=0.244  Sum_probs=179.1

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChh---hccccCccccCCCCcccc---C-
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSA---SGNGLLHYSVPNGAGTVA---G-  143 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~---~a~~~~~~~l~n~~~~~~---g-  143 (818)
                      ...+++-.|.....+-++.++|+..|.|   .+..|..+.+++|++++.|.+..   .+..+.+..+..-+..+.   . 
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEae  258 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAE  258 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHH
Confidence            3567888888888899999999999976   57789999999999999999765   233333333332211110   0 


Q ss_pred             ----------CC-CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHH
Q 003463          144 ----------EH-PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR  207 (818)
Q Consensus       144 ----------~~-~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~  207 (818)
                                .. .....|-+.|||+||..+++|++|+.+|+.||.|..|..     ++.++||+||+|.+.++|++|+.
T Consensus       259 knr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e  338 (549)
T KOG0147|consen  259 KNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALE  338 (549)
T ss_pred             HHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHH
Confidence                      00 011234455999999999999999999999999999872     78899999999999999999999


Q ss_pred             HhcCcccccccccccccCCCCCCCCC-------C----------------------------------------------
Q 003463          208 ALQNKPLRRRKLDIHFSIPKDNPSDK-------D----------------------------------------------  234 (818)
Q Consensus       208 ~Lng~~l~gr~L~V~~a~pk~~~~~~-------~----------------------------------------------  234 (818)
                      .|||..|.|+.|+|.....+-.....       +                                              
T Consensus       339 ~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~  418 (549)
T KOG0147|consen  339 QLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASA  418 (549)
T ss_pred             HhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchH
Confidence            99999999999988643211100000       0                                              


Q ss_pred             ----------------------CCccceeeecCCCC--CC--------HHHHHHHhhccCCeEEEEecCCCCceEEEEEc
Q 003463          235 ----------------------LNQGTLVVFNLDPS--VS--------NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY  282 (818)
Q Consensus       235 ----------------------~~~~tL~V~NLp~~--vt--------eedL~~lFs~fG~I~~vr~~g~srG~aFVeF~  282 (818)
                                            +...++.++|+=..  .|        .||+.+.+.+||.|..|.+...+-|+.||.|.
T Consensus       419 ~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~  498 (549)
T KOG0147|consen  419 AQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCP  498 (549)
T ss_pred             HhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecC
Confidence                                  00113344444211  11        37888899999999999998888899999999


Q ss_pred             CHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          283 DVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       283 d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      +.++|..|+++|||.+|.||.|++.|-.
T Consensus       499 s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  499 SAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             cHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            9999999999999999999999999853

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.71  E-value=1.5e-16  Score=161.13  Aligned_cols=162  Identities=27%  Similarity=0.457  Sum_probs=142.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHH----HhhcCCCEEEEE--eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRA----LFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~----lFs~fG~I~~v~--~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ..++.||||+||+..+..++|++    +|++||.|.+|.  .+.+.+|-|||.|.+.+.|-.|+++|+|..+.|++++|+
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            34667999999999999999988    999999999998  367899999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCC----------------------------------------------CCCccceeeecCCCCCCHHHHHH
Q 003463          223 FSIPKDNPSDK----------------------------------------------DLNQGTLVVFNLDPSVSNEDLRQ  256 (818)
Q Consensus       223 ~a~pk~~~~~~----------------------------------------------~~~~~tL~V~NLp~~vteedL~~  256 (818)
                      |+..+.+...+                                              ......|++.|||.+++.+.|..
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            98654321111                                              12235799999999999999999


Q ss_pred             HhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC-CceEEEEecC
Q 003463          257 IFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSR  310 (818)
Q Consensus       257 lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~  310 (818)
                      +|.+|.-.++|+......+.|||+|.+...|..|...|.|..|. ...++|.+++
T Consensus       166 lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999988778899999999999999999999999887 7889988875

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=1.3e-17  Score=170.49  Aligned_cols=167  Identities=23%  Similarity=0.434  Sum_probs=138.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcc-ccc--ccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKP-LRR--RKLDIHF  223 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~-l~g--r~L~V~~  223 (818)
                      ..|+|||+-|.+.-.|||++.+|..||.|.+|.+    .+.+||+|||.|.+..+|+.||..|+|.. +-|  ..|.|+|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            5789999999999999999999999999999973    67799999999999999999999999854 222  2333333


Q ss_pred             cCCCCCCC------------------------------------------------------------------------
Q 003463          224 SIPKDNPS------------------------------------------------------------------------  231 (818)
Q Consensus       224 a~pk~~~~------------------------------------------------------------------------  231 (818)
                      ++..+++.                                                                        
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            22211000                                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q 003463          232 --------------------------------------------------------------------------------  231 (818)
Q Consensus       232 --------------------------------------------------------------------------------  231 (818)
                                                                                                      
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence                                                                                            


Q ss_pred             ----------------------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCH
Q 003463          232 ----------------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDV  284 (818)
Q Consensus       232 ----------------------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~  284 (818)
                                            .+....++|||..||.+..+.||.++|-+||.|++.++     +..+|+|+||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                                  00001158999999999999999999999999998753     778999999999999


Q ss_pred             HHHHHHHHHcCCCccCCceEEEEecCCCcccch
Q 003463          285 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN  317 (818)
Q Consensus       285 e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r~~  317 (818)
                      .+|+.||.+|||..|+-|+|+|...+|+...|.
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanRP  370 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDANRP  370 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccccCCC
Confidence            999999999999999999999999999987653

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.69  E-value=1.8e-14  Score=155.82  Aligned_cols=159  Identities=24%  Similarity=0.391  Sum_probs=132.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhh-cCCCEEEEE----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFE-QYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs-~fG~I~~v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .|.+||.|||+++...+|++||. +.|+|+.|.    ..+|.+|+|.|+|+++|.+++|++.|+...+.||+|.|+-...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            46799999999999999999997 689999987    4789999999999999999999999999999999998864211


Q ss_pred             CCC------------------------------------------CCCCC------------------------------
Q 003463          227 KDN------------------------------------------PSDKD------------------------------  234 (818)
Q Consensus       227 k~~------------------------------------------~~~~~------------------------------  234 (818)
                      .+.                                          +.+++                              
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence            000                                          00000                              


Q ss_pred             ---------CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC
Q 003463          235 ---------LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  301 (818)
Q Consensus       235 ---------~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G  301 (818)
                               +...++||.||.+.+..+.|++.|.-.|.|..|.+    .+.++|+|.|+|+.+-+|..||..|++.-+..
T Consensus       204 lr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~  283 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFD  283 (608)
T ss_pred             hhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCcc
Confidence                     01137899999999999999999999999988853    46788999999999999999999999988888


Q ss_pred             ceEEEEecC
Q 003463          302 KRIKLEPSR  310 (818)
Q Consensus       302 r~L~V~~a~  310 (818)
                      ++..+...+
T Consensus       284 ~~~~~Rl~~  292 (608)
T KOG4212|consen  284 RRMTVRLDR  292 (608)
T ss_pred             ccceeeccc
Confidence            888887754

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=4.9e-16  Score=164.54  Aligned_cols=151  Identities=13%  Similarity=0.229  Sum_probs=122.8

Q ss_pred             CccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCC
Q 003463           73 IMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH  145 (818)
Q Consensus        73 v~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~  145 (818)
                      +|+++||+.+...+.|+.++..|..||.|   ...-|+.|+..+||+||.|.-.++|.    .+++..+-++.+++....
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            48899999999999999999999999987   46678999999999999999777553    444444433333332211


Q ss_pred             CC------------CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHH
Q 003463          146 PY------------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRA  208 (818)
Q Consensus       146 ~~------------~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~  208 (818)
                      ..            ..+.-.+|||..+.++.+|+||+..|+.||+|..|..     .+.++||+||+|.+......|+..
T Consensus       192 NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            11            1123468999999999999999999999999999983     567999999999999999999999


Q ss_pred             hcCcccccccccccc
Q 003463          209 LQNKPLRRRKLDIHF  223 (818)
Q Consensus       209 Lng~~l~gr~L~V~~  223 (818)
                      +|-..+.|+.|+|..
T Consensus       272 MNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGK  286 (544)
T ss_pred             cchhhcccceEeccc
Confidence            999999988887754

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.65  E-value=2e-15  Score=162.49  Aligned_cols=237  Identities=22%  Similarity=0.307  Sum_probs=172.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhccccCccccCCC----------------
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNG----------------  137 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~~~~~~~l~n~----------------  137 (818)
                      ..-+.+|+||++++|.|+..++..+|.|.-   ...-+.+-.+|+.|++.+.|..++.|...-.                
T Consensus        28 SkV~HlRnlp~e~tE~elI~Lg~pFG~vtn---~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn~~  104 (492)
T KOG1190|consen   28 SKVVHLRNLPWEVTEEELISLGLPFGKVTN---LLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSNHS  104 (492)
T ss_pred             cceeEeccCCccccHHHHHHhcccccceee---eeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehhhhHH
Confidence            456889999999999999999999998720   0011122245666666655544222211000                


Q ss_pred             -------Cc-------------------cccC--CCC-CCCCCC--cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCC
Q 003463          138 -------AG-------------------TVAG--EHP-YGEHPS--RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC  186 (818)
Q Consensus       138 -------~~-------------------~~~g--~~~-~~e~~s--rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~  186 (818)
                             +.                   ....  ... ....++  -+++|.++-+.|+-+-|..+|++||.|..|.+..
T Consensus       105 ~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~  184 (492)
T KOG1190|consen  105 ELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFT  184 (492)
T ss_pred             HHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEe
Confidence                   00                   0000  000 011122  2567899999999999999999999999998888


Q ss_pred             CcccE-EEEEEccHHHHHHHHHHhcCcccc--cccccccccCC----------CCC-------CCC--------------
Q 003463          187 KHRGF-VMISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIP----------KDN-------PSD--------------  232 (818)
Q Consensus       187 ksrG~-AFV~F~d~e~A~~Al~~Lng~~l~--gr~L~V~~a~p----------k~~-------~~~--------------  232 (818)
                      |..|| |.|+|.|.+.|+.|...|+|+.|.  .+.|+|.|+.-          +.+       +..              
T Consensus       185 Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~  264 (492)
T KOG1190|consen  185 KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAF  264 (492)
T ss_pred             cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccc
Confidence            88887 999999999999999999999885  35666665421          110       000              


Q ss_pred             --------------------------CCC--CccceeeecCCC-CCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcC
Q 003463          233 --------------------------KDL--NQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYD  283 (818)
Q Consensus       233 --------------------------~~~--~~~tL~V~NLp~-~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d  283 (818)
                                                -..  ....|.|.||.. .+|.+-|..+|+.||+|.+|++.-+++..|.|+|.|
T Consensus       265 ~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd  344 (492)
T KOG1190|consen  265 GSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSD  344 (492)
T ss_pred             cccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecc
Confidence                                      000  024677888875 579999999999999999999877777899999999


Q ss_pred             HHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          284 VRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       284 ~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...|+-|+..|+|..+.||+|+|.+++...
T Consensus       345 ~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  345 GQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             hhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            999999999999999999999999998754

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.61  E-value=3.1e-16  Score=174.82  Aligned_cols=162  Identities=23%  Similarity=0.376  Sum_probs=139.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      .++..||+|+--|+..++..+|.++|+.+|+|..|.     .++.++|.|||+|.|.+....|+. |.|..+.|.+|.|+
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            345568999999999999999999999999999987     366799999999999999999996 99999999999998


Q ss_pred             ccCCCCCCCCC----------CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHH
Q 003463          223 FSIPKDNPSDK----------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAA  287 (818)
Q Consensus       223 ~a~pk~~~~~~----------~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A  287 (818)
                      .....++....          ...-..|||+||...+++++|+.+|++||.|..|.+     ++.++||+||+|.+.++|
T Consensus       254 ~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~a  333 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDA  333 (549)
T ss_pred             ccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHH
Confidence            76443322110          011123999999999999999999999999999853     788999999999999999


Q ss_pred             HHHHHHcCCCccCCceEEEEecC
Q 003463          288 EAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       288 ~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      .+|+..|||.+|.|+.|+|....
T Consensus       334 r~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  334 RKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             HHHHHHhccceecCceEEEEEee
Confidence            99999999999999999997653

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.60  E-value=1.9e-15  Score=163.35  Aligned_cols=162  Identities=18%  Similarity=0.397  Sum_probs=141.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||++|++++++|.|++.|.+||+|..|.+     +++++||+||+|.+.+...+++. .....|.|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            5789999999999999999999999999999873     67899999999999999999987 46788999999999988


Q ss_pred             CCCCCCCCCC--CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          226 PKDNPSDKDL--NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       226 pk~~~~~~~~--~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ++........  ...+|||++||.+++++++++.|.+||.|..+.     .+.+.++|+||.|++++++.+++. ..-+.
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~  162 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHD  162 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceee
Confidence            8775443322  356899999999999999999999999887763     255679999999999999999886 67889


Q ss_pred             cCCceEEEEecCCCcc
Q 003463          299 IAGKRIKLEPSRPGGA  314 (818)
Q Consensus       299 i~Gr~L~V~~a~~~~~  314 (818)
                      |.|+.+.|.-|.|+..
T Consensus       163 ~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEV  178 (311)
T ss_pred             ecCceeeEeeccchhh
Confidence            9999999999988763

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=1.3e-14  Score=142.06  Aligned_cols=149  Identities=22%  Similarity=0.329  Sum_probs=126.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCC--cccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~k--srG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ..+++|||+|||.++.+.||.++|-+||.|..|.+...  .-.||||+|++..+|+.||..-+|..+.|..|+|+|+...
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            45789999999999999999999999999999986444  3469999999999999999999999999999999997543


Q ss_pred             CCCCC----------------------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHH
Q 003463          228 DNPSD----------------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR  285 (818)
Q Consensus       228 ~~~~~----------------------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e  285 (818)
                      .....                      ....+..+.|++||++.+.+||++...+-|.|....+..  .+++.|+|...|
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r--Dg~GvV~~~r~e  161 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR--DGVGVVEYLRKE  161 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeec--ccceeeeeeehh
Confidence            21110                      011234799999999999999999999999998887754  468999999999


Q ss_pred             HHHHHHHHcCCCccC
Q 003463          286 AAEAALKSLNRSDIA  300 (818)
Q Consensus       286 ~A~~Ai~~LnG~~i~  300 (818)
                      +.+-|++.|+...+.
T Consensus       162 DMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  162 DMKYAVRKLDDQKFR  176 (241)
T ss_pred             hHHHHHHhhcccccc
Confidence            999999999887665

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=4.8e-14  Score=161.11  Aligned_cols=191  Identities=25%  Similarity=0.373  Sum_probs=153.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC--
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP--  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p--  226 (818)
                      +...+.|+|+|||..+..++|...|..||+|..+.+. ...--++|.|.+..+|++|++.|....+...++++.++..  
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp-~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dv  460 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP-PGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDV  460 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecC-cccceeeeeecCccchHHHHHHhchhhhccCccccccChhhh
Confidence            3445789999999999999999999999999998543 3333499999999999999999999999888887766421  


Q ss_pred             -----CCC-------------CCC------------CC-------------CCc-cceeeecCCCCCCHHHHHHHhhccC
Q 003463          227 -----KDN-------------PSD------------KD-------------LNQ-GTLVVFNLDPSVSNEDLRQIFGAYG  262 (818)
Q Consensus       227 -----k~~-------------~~~------------~~-------------~~~-~tL~V~NLp~~vteedL~~lFs~fG  262 (818)
                           +..             +..            .+             ... .+|||.||++++|.++|...|..+|
T Consensus       461 f~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G  540 (725)
T KOG0110|consen  461 FTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQG  540 (725)
T ss_pred             ccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcC
Confidence                 100             000            00             011 2499999999999999999999999


Q ss_pred             CeEEEEecCC--------CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC--------C---cc--cchhhhc
Q 003463          263 EVKEIRETPH--------KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP--------G---GA--RRNLMLQ  321 (818)
Q Consensus       263 ~I~~vr~~g~--------srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~--------~---~~--r~~~~~q  321 (818)
                      .|..+.+..+        +.|||||+|.+.++|+.|++.|+|+.|+|+.|.|+++..        +   ..  .+.++++
T Consensus       541 ~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRN  620 (725)
T KOG0110|consen  541 TVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRN  620 (725)
T ss_pred             eEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeec
Confidence            9999966322        349999999999999999999999999999999999871        1   11  1347788


Q ss_pred             cchhccHHHHHHHHhhcCC
Q 003463          322 LNQELEQDESRILQHQVGS  340 (818)
Q Consensus       322 l~~~~~~~~l~~~f~~~Gs  340 (818)
                      ++-+.+..+++.+|..||.
T Consensus       621 ipFeAt~rEVr~LF~aFGq  639 (725)
T KOG0110|consen  621 IPFEATKREVRKLFTAFGQ  639 (725)
T ss_pred             cchHHHHHHHHHHHhcccc
Confidence            8889999999999999983

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.49  E-value=6.5e-13  Score=143.39  Aligned_cols=160  Identities=26%  Similarity=0.359  Sum_probs=136.4

Q ss_pred             CcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCC
Q 003463          152 SRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  230 (818)
Q Consensus       152 srtLfV~NLP~~-vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~  230 (818)
                      +..|.|.||..+ ||.+.|..+|.-||+|.+|++..+.+--|.|+|.|...|+-|++.|+|..+.|++|+|.+++.....
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            478889998654 9999999999999999999987777789999999999999999999999999999999988643211


Q ss_pred             CCC----C---------------------------CCccceeeecCCCCCCHHHHHHHhhccCCe-EEEEecCCCCceEE
Q 003463          231 SDK----D---------------------------LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-KEIRETPHKRHHKF  278 (818)
Q Consensus       231 ~~~----~---------------------------~~~~tL~V~NLp~~vteedL~~lFs~fG~I-~~vr~~g~srG~aF  278 (818)
                      ..+    +                           ....+|.+.|+|.+++||||+..|..-|-. +..+..++.+.+|+
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal  456 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMAL  456 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceee
Confidence            100    0                           122489999999999999999999988755 55677777788999


Q ss_pred             EEEcCHHHHHHHHHHcCCCccCC-ceEEEEecCC
Q 003463          279 IEFYDVRAAEAALKSLNRSDIAG-KRIKLEPSRP  311 (818)
Q Consensus       279 VeF~d~e~A~~Ai~~LnG~~i~G-r~L~V~~a~~  311 (818)
                      +++.++|+|..|+..++.+.+++ ..|+|+|++.
T Consensus       457 ~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  457 PQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            99999999999999999999986 5999999875

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.49  E-value=5.6e-14  Score=146.06  Aligned_cols=147  Identities=21%  Similarity=0.329  Sum_probs=124.4

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYGE  149 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~~~e  149 (818)
                      +.++||+|||...++.++..+|..+|.| |+.|.    .|.|+||++.+..++.    -+.+|++.+..+.++..+.. .
T Consensus         2 ~~KLFIGNLp~~~~~~elr~lFe~ygkV-lECDI----vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK-s   75 (346)
T KOG0109|consen    2 PVKLFIGNLPREATEQELRSLFEQYGKV-LECDI----VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK-S   75 (346)
T ss_pred             ccchhccCCCcccchHHHHHHHHhhCce-Eeeee----ecccceEEeecccccHHHHhhcccceecceEEEEEecccc-C
Confidence            4679999999999999999999999988 33332    3468999998876544    36778887776666554443 5


Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      +.+++|+|+||.+.++.+||+..|++||.|..|++   -++|+||.|+-.++|..|++.|++..+.|++++|+.+..+-.
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdi---vkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDI---VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeee---ecceeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence            67899999999999999999999999999999976   478999999999999999999999999999999999876543

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.45  E-value=8.2e-14  Score=142.59  Aligned_cols=150  Identities=26%  Similarity=0.430  Sum_probs=129.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCC-
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS-  231 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~-  231 (818)
                      ..+||++||+.+.+++|..+|..||.|..+.+   ..||+||+|.+..+|+.|+..|++..|.+..+.|.++....... 
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m---k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g   78 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM---KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRG   78 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee---ecccceeccCchhhhhcccchhcCceecceeeeeecccccccccC
Confidence            46999999999999999999999999999865   35889999999999999999999999999888888887421100 


Q ss_pred             ---------------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCC
Q 003463          232 ---------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR  296 (818)
Q Consensus       232 ---------------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG  296 (818)
                                     ........|.|.++...+.+.+|.+.|.++|.+.....   ..+++||+|...++|.+|+..|++
T Consensus        79 ~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~  155 (216)
T KOG0106|consen   79 RPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDG  155 (216)
T ss_pred             CCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccc
Confidence                           01223457889999999999999999999999955554   578999999999999999999999


Q ss_pred             CccCCceEEEEe
Q 003463          297 SDIAGKRIKLEP  308 (818)
Q Consensus       297 ~~i~Gr~L~V~~  308 (818)
                      .++.++.|++..
T Consensus       156 ~~~~~~~l~~~~  167 (216)
T KOG0106|consen  156 KKLNGRRISVEK  167 (216)
T ss_pred             hhhcCceeeecc
Confidence            999999999943

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.44  E-value=5.8e-13  Score=133.95  Aligned_cols=150  Identities=21%  Similarity=0.347  Sum_probs=115.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE--EeCCCc----ccEEEEEEccHHHHHHHHHHhcCcccc---cccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL--YTACKH----RGFVMISYYDIRAARTAMRALQNKPLR---RRKLDI  221 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v--~~~~ks----rG~AFV~F~d~e~A~~Al~~Lng~~l~---gr~L~V  221 (818)
                      .-|||||.+||.++...||..+|..|--.+.+  +.+.+.    +-+|||.|.+..+|..|+.+|||..++   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            46999999999999999999999988654443  333333    479999999999999999999999986   667777


Q ss_pred             cccCCCCCCCCC---------------------------------------------------CC---------------
Q 003463          222 HFSIPKDNPSDK---------------------------------------------------DL---------------  235 (818)
Q Consensus       222 ~~a~pk~~~~~~---------------------------------------------------~~---------------  235 (818)
                      ++++......+.                                                   +.               
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            765432110000                                                   00               


Q ss_pred             ----------------CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCC-CCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          236 ----------------NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-KRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       236 ----------------~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~-srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                                      ...||||-||.+++||++|+++|+.|-.....++..+ ....||++|++.+.|..|+..|.|..
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~  272 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNL  272 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcce
Confidence                            0038999999999999999999999976555555322 23579999999999999999999876


Q ss_pred             cC
Q 003463          299 IA  300 (818)
Q Consensus       299 i~  300 (818)
                      |.
T Consensus       273 ~s  274 (284)
T KOG1457|consen  273 LS  274 (284)
T ss_pred             ec
Confidence            64

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.42  E-value=5.8e-12  Score=134.61  Aligned_cols=231  Identities=18%  Similarity=0.267  Sum_probs=171.2

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE------------EEeecCCCCCcccEEEEEecChhhc-----cccCccccCCC
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGM------------ELEGEPQESLSMSMSKISISDSASG-----NGLLHYSVPNG  137 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i------------~V~~d~~t~~skG~a~v~f~~~~~a-----~~~~~~~l~n~  137 (818)
                      --+.||+|-..+.|.++.+..+.+|.|            .|+|++.+++   ..-|+|+....-     ..+.+|.... 
T Consensus        32 pvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~a---kn~Vnfaa~n~i~i~gq~Al~NyStsq-  107 (494)
T KOG1456|consen   32 PVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGA---KNCVNFAADNQIYIAGQQALFNYSTSQ-  107 (494)
T ss_pred             ceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccch---hhheehhccCcccccCchhhcccchhh-
Confidence            347899999999999999999999987            2444443332   222333322110     0122221111 


Q ss_pred             CccccCCCCCCCCCCcEEEEcCC--CCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          138 AGTVAGEHPYGEHPSRTLFVRNI--NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       138 ~~~~~g~~~~~e~~srtLfV~NL--P~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                        ++.........++..|.+.=|  =+.+|-+-|..+....|+|.+|.+..|.--.|+|+|++.+.|++|..+|||..|.
T Consensus       108 --~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIY  185 (494)
T KOG1456|consen  108 --CIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIY  185 (494)
T ss_pred             --hhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhccccccc
Confidence              122222333455666665544  4668999999999999999999988887678999999999999999999998885


Q ss_pred             --cccccccccCCCCCCCCCC-----------------------------------------------------------
Q 003463          216 --RRKLDIHFSIPKDNPSDKD-----------------------------------------------------------  234 (818)
Q Consensus       216 --gr~L~V~~a~pk~~~~~~~-----------------------------------------------------------  234 (818)
                        ..+|+|+|++|.+....+.                                                           
T Consensus       186 sGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P  265 (494)
T KOG1456|consen  186 SGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPP  265 (494)
T ss_pred             ccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCC
Confidence              5789999987753110000                                                           


Q ss_pred             -------------------CCccceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc
Q 003463          235 -------------------LNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL  294 (818)
Q Consensus       235 -------------------~~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L  294 (818)
                                         .....+.|.+|+.. +.-+.|..+|-.||.|.+|++...+.|.|+||+.|..+.++|+..|
T Consensus       266 ~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hL  345 (494)
T KOG1456|consen  266 SRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHL  345 (494)
T ss_pred             CCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHh
Confidence                               00126889999865 5778999999999999999998888899999999999999999999


Q ss_pred             CCCccCCceEEEEecCC
Q 003463          295 NRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       295 nG~~i~Gr~L~V~~a~~  311 (818)
                      |+..+.|.+|.|.+++.
T Consensus       346 nn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  346 NNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             ccCccccceEEEeeccc
Confidence            99999999999999863

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.41  E-value=8.9e-13  Score=128.83  Aligned_cols=78  Identities=24%  Similarity=0.453  Sum_probs=71.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+.+|+++|+++|++||.|++|++     ++++++||||+|.+.++|++|++.||+..|.|++|+|++++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            3468999999999999999999999999999865     45679999999999999999999999999999999999987


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus       113 ~~~  115 (144)
T PLN03134        113 DRP  115 (144)
T ss_pred             cCC
Confidence            654

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.39  E-value=1.2e-11  Score=134.19  Aligned_cols=70  Identities=23%  Similarity=0.292  Sum_probs=64.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ++|+|+|||.++|++.|++-|..||.|..+++  .++++  +.|+|.++++|++|+..|+|..+.|+.|+|.|.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~Gksk--GVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSK--GVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhccCCcc--ceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            37999999999999999999999999999887  55555  599999999999999999999999999999873

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.39  E-value=1.7e-12  Score=126.80  Aligned_cols=80  Identities=24%  Similarity=0.439  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ...+++|||+|||.+++|++|+++|++||.|.+|.+     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            345789999999999999999999999999999874     567899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003463          224 SIPKD  228 (818)
Q Consensus       224 a~pk~  228 (818)
                      +.++.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            87654

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.33  E-value=1.5e-12  Score=127.80  Aligned_cols=155  Identities=16%  Similarity=0.260  Sum_probs=128.4

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccC--CC
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAG--EH  145 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g--~~  145 (818)
                      ..+||++|+..+++.-++++|-+.|.|   .+..|..+...+||+|+.|.+.+.|.    .++..++-+.++++..  .+
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~   89 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAH   89 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccc
Confidence            468999999999999999999999965   67888889999999999999887664    3444455565555432  23


Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE---E---eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL---Y---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v---~---~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      ...-....+|||+||.+.++|..|.+.|+.||.+...   .   .++..+||+||.|.+.+.+.+|++.++|+.+..+++
T Consensus        90 ~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~i  169 (203)
T KOG0131|consen   90 QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPI  169 (203)
T ss_pred             cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCce
Confidence            3333455799999999999999999999999987652   1   467899999999999999999999999999999999


Q ss_pred             cccccCCCCC
Q 003463          220 DIHFSIPKDN  229 (818)
Q Consensus       220 ~V~~a~pk~~  229 (818)
                      .|.++..+..
T Consensus       170 tv~ya~k~~~  179 (203)
T KOG0131|consen  170 TVSYAFKKDT  179 (203)
T ss_pred             EEEEEEecCC
Confidence            9999876544

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.31  E-value=4e-11  Score=127.76  Aligned_cols=164  Identities=15%  Similarity=0.238  Sum_probs=132.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE--------E----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL--------Y----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  217 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v--------~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr  217 (818)
                      .-++.|||.|||.++|.+++.++|++||-|..-        +    ..|+-+|-|.+.|...++++-|++.|++..++|+
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            345679999999999999999999999987542        2    2577899999999999999999999999999999


Q ss_pred             cccccccCCCCC--------C--------------------------CCCCCCccceeeecCCC----CCC-------HH
Q 003463          218 KLDIHFSIPKDN--------P--------------------------SDKDLNQGTLVVFNLDP----SVS-------NE  252 (818)
Q Consensus       218 ~L~V~~a~pk~~--------~--------------------------~~~~~~~~tL~V~NLp~----~vt-------ee  252 (818)
                      +|+|+.|.-...        .                          ..+....++|.|.|+=.    ..+       ++
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            999987632110        0                          00111235888988842    222       46


Q ss_pred             HHHHHhhccCCeEEEEe-cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          253 DLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       253 dL~~lFs~fG~I~~vr~-~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      +|++-+++||.|.+|.+ ...+.|.+-|.|.+.++|..||+.|+|+.+.||+|..+....+.
T Consensus       292 dl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             HHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcc
Confidence            77788999999999976 45678999999999999999999999999999999998876543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.30  E-value=7.8e-12  Score=135.53  Aligned_cols=190  Identities=15%  Similarity=0.225  Sum_probs=135.5

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhh-ccccC--ccccCCCCccc------
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSAS-GNGLL--HYSVPNGAGTV------  141 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~-a~~~~--~~~l~n~~~~~------  141 (818)
                      ..++||++|.|+.+++.|.+.|.++|.+   .|+.|..+++++||+||+|++.+. ...+.  ...+.......      
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r   85 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSR   85 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCc
Confidence            4789999999999999999999999987   488899999999999999996542 22211  12222221111      


Q ss_pred             -cCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          142 -AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       142 -~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                       ..........+.+|||++||.+++++++++.|++||.|..+.     .+.+.+||+||.|.+.+.+++++. ..-+.|.
T Consensus        86 ~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~  164 (311)
T KOG4205|consen   86 EDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFN  164 (311)
T ss_pred             ccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeec
Confidence             111112222466999999999999999999999999887775     367789999999999999999988 5788999


Q ss_pred             cccccccccCCCCCCCCCCCCc-cceeeecCCCCCCHHHHHHHhhccCCe
Q 003463          216 RRKLDIHFSIPKDNPSDKDLNQ-GTLVVFNLDPSVSNEDLRQIFGAYGEV  264 (818)
Q Consensus       216 gr~L~V~~a~pk~~~~~~~~~~-~tL~V~NLp~~vteedL~~lFs~fG~I  264 (818)
                      ++.+.|..+.|++......... ......++....+.-.|...|.-|+.+
T Consensus       165 gk~vevkrA~pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~  214 (311)
T KOG4205|consen  165 GKKVEVKRAIPKEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPV  214 (311)
T ss_pred             CceeeEeeccchhhccccccccccccccccccccccccccchhccccCcc
Confidence            9999999999887543322111 112222344344444455555555544

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.28  E-value=2.7e-11  Score=134.27  Aligned_cols=156  Identities=18%  Similarity=0.284  Sum_probs=124.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE---eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~---~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      .--|-+++||+++|++||.++|+.++ |+.+.   .+++..|-|||+|.+.+++++|++ .+...+..+-|.|-.+.+++
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCcc
Confidence            34677899999999999999999986 55554   468899999999999999999999 58888888888887664443


Q ss_pred             CCC-------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEE-EE----ecCCCCceEEEEEcCHHHHHHHHHHcCC
Q 003463          229 NPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IR----ETPHKRHHKFIEFYDVRAAEAALKSLNR  296 (818)
Q Consensus       229 ~~~-------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~-vr----~~g~srG~aFVeF~d~e~A~~Ai~~LnG  296 (818)
                      ...       ........|.+++||+.+|++||.++|+..-.|.. |-    -.+++.|-|||+|++.+.|++|+.. |.
T Consensus        88 ~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hr  166 (510)
T KOG4211|consen   88 ADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HR  166 (510)
T ss_pred             ccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HH
Confidence            211       11135568999999999999999999998755444 21    2345678999999999999999984 66


Q ss_pred             CccCCceEEEEecC
Q 003463          297 SDIAGKRIKLEPSR  310 (818)
Q Consensus       297 ~~i~Gr~L~V~~a~  310 (818)
                      ..|.-|-|.|-.+.
T Consensus       167 e~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  167 ENIGHRYIEVFRSS  180 (510)
T ss_pred             HhhccceEEeehhH
Confidence            77887888887664

>PF00076 RRM_1: RNA recognition motif

Probab=99.26  E-value=8.7e-12  Score=104.86  Aligned_cols=66  Identities=36%  Similarity=0.634  Sum_probs=61.2

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       240 L~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      |||+|||.++|+++|+++|++||.|..+++.    +..+++|||+|.+.++|++|++.|+|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999988653    45688999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=8.3e-12  Score=121.95  Aligned_cols=77  Identities=30%  Similarity=0.475  Sum_probs=72.8

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+||+..+++.||+.+|..||.|..|.+.....|||||||+|..+|+.|+..|+|+.|.|.+|+|+++.-..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            56899999999999999999999999999999888889999999999999999999999999999999999987544

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=6.7e-11  Score=134.21  Aligned_cols=236  Identities=15%  Similarity=0.258  Sum_probs=160.3

Q ss_pred             cccccccCCCCCChHHHHHhhcCC-----------CcEEEeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCcc
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSG-----------GGMELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGT  140 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~-----------G~i~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~~  140 (818)
                      ..+++.+++..+.+.....+|..-           |.-+|..  .....+.++++.|.....+.   ........+...+
T Consensus       176 ~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~--~~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~  253 (500)
T KOG0120|consen  176 RRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSV--QLNLEKNFAFIEFRSISEATEAMALDGIIFEGRPLK  253 (500)
T ss_pred             hhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeee--eecccccceeEEecCCCchhhhhcccchhhCCCCce
Confidence            458899999999999988888763           2212211  12344556677666543221   1111111111000


Q ss_pred             ------------------------ccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccE
Q 003463          141 ------------------------VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGF  191 (818)
Q Consensus       141 ------------------------~~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~  191 (818)
                                              .....+........+||++||..+++.+++++.+.||+++...     .++.++||
T Consensus       254 ~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~  333 (500)
T KOG0120|consen  254 IRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGF  333 (500)
T ss_pred             ecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccce
Confidence                                    0111122223456899999999999999999999999987765     35689999


Q ss_pred             EEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCCCC--------------------CCccceeeecCCC--CC
Q 003463          192 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD--------------------LNQGTLVVFNLDP--SV  249 (818)
Q Consensus       192 AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~--------------------~~~~tL~V~NLp~--~v  249 (818)
                      ||.+|.+......|+..|+|+.+.+++|.|+.+.+........                    .....|.+.|+=.  ++
T Consensus       334 af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deL  413 (500)
T KOG0120|consen  334 AFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDEL  413 (500)
T ss_pred             eeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHh
Confidence            9999999999999999999999999999998875543211111                    1112233333310  00


Q ss_pred             -CH-------HHHHHHhhccCCeEEEEecCC--------CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          250 -SN-------EDLRQIFGAYGEVKEIRETPH--------KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       250 -te-------edL~~lFs~fG~I~~vr~~g~--------srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                       .+       |+++..+.+||.|..|.+...        ..|..||||.+.+++++|..+|+|.++.|+.|...|....
T Consensus       414 kdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  414 KDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             cchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence             11       556677889999999965321        3567899999999999999999999999999999997643

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.25  E-value=3.8e-11  Score=128.80  Aligned_cols=235  Identities=13%  Similarity=0.157  Sum_probs=154.7

Q ss_pred             cccccCCCCCChHHHHHhhcC----CCcEEEeecCCCCCcccEEEEEecChhhcc---ccCccccCCCC-----------
Q 003463           77 FDLRGLPSSLEDLEDYDIFGS----GGGMELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGA-----------  138 (818)
Q Consensus        77 ~~V~~Lp~s~~E~el~diF~~----~G~i~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~-----------  138 (818)
                      +-.|+|||+-.+.++..+|.-    .|++-++.. ..++-.|.+.+.|.+.+.-.   +.....+....           
T Consensus        63 vRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~-~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~f  141 (508)
T KOG1365|consen   63 VRARGLPWQSSDQDIARFFKGLNIANGGRALCLN-AQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEEF  141 (508)
T ss_pred             EEecCCCCCcccCCHHHHHhhhhccccceeeeeh-hhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchhh
Confidence            445999999999999888874    334444432 35666788888888755221   11111111110           


Q ss_pred             ccc------cCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcC-----CC--EEEEE-eCCCcccEEEEEEccHHHHHH
Q 003463          139 GTV------AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQY-----GD--IRTLY-TACKHRGFVMISYYDIRAART  204 (818)
Q Consensus       139 ~~~------~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~f-----G~--I~~v~-~~~ksrG~AFV~F~d~e~A~~  204 (818)
                      .++      ...........-.|-+++||+++++.++.++|..-     |.  |.-|. ..++-.|-|||.|..+++|+.
T Consensus       142 ~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~  221 (508)
T KOG1365|consen  142 LKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQF  221 (508)
T ss_pred             eEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHH
Confidence            001      11111111223456779999999999999999622     22  33333 378889999999999999999


Q ss_pred             HHHHhcCcccccccccccccCCC---------------------------CCCCCCCCCccceeeecCCCCCCHHHHHHH
Q 003463          205 AMRALQNKPLRRRKLDIHFSIPK---------------------------DNPSDKDLNQGTLVVFNLDPSVSNEDLRQI  257 (818)
Q Consensus       205 Al~~Lng~~l~gr~L~V~~a~pk---------------------------~~~~~~~~~~~tL~V~NLp~~vteedL~~l  257 (818)
                      |+.+ +...|..|.|.+-.+...                           ...........+|.+++||++.+.|||.++
T Consensus       222 aL~k-hrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~F  300 (508)
T KOG1365|consen  222 ALRK-HRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDF  300 (508)
T ss_pred             HHHH-HHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHH
Confidence            9985 555555554443221000                           000111223568999999999999999999


Q ss_pred             hhccCCeEE---EE----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          258 FGAYGEVKE---IR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       258 Fs~fG~I~~---vr----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      |..|-.-++   |.    -.++..|-|||+|.+.++|..|....+++..++|.|.|-.+....
T Consensus       301 lgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~ee  363 (508)
T KOG1365|consen  301 LGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEE  363 (508)
T ss_pred             HHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHH
Confidence            998853222   32    246677899999999999999999988888889999998775544

>PF00076 RRM_1: RNA recognition motif

Probab=99.24  E-value=1.6e-11  Score=103.26  Aligned_cols=66  Identities=29%  Similarity=0.603  Sum_probs=61.5

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          155 LFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       155 LfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      |||+|||.++|+++|+++|++||.|..+.+    .++.+|+|||+|.+.++|++|++.|+|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999988873    456899999999999999999999999999999874

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.23  E-value=7.8e-11  Score=130.63  Aligned_cols=230  Identities=14%  Similarity=0.172  Sum_probs=155.5

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhcc---ccCccccCCC----------Cccc
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNG----------AGTV  141 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~----------~~~~  141 (818)
                      -.+-|++|||+|+++|+.++|++++.-.+++-..+++..|-++|.|...+...   +.....+.+.          ....
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~   90 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADW   90 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccc
Confidence            55778999999999999999999886556677778999999999999766432   2211112111          0000


Q ss_pred             --cCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE-E----EeCCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          142 --AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-L----YTACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       142 --~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~-v----~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                        ....+........|-+++||+.||++||.++|+..-.|.. |    ...++..|-|||+|.+.+.|++|+.. +...|
T Consensus        91 ~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~i  169 (510)
T KOG4211|consen   91 VMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENI  169 (510)
T ss_pred             cccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhh
Confidence              0011112235568999999999999999999996643333 1    12466889999999999999999984 55555


Q ss_pred             cccccccccc-----------------------CCCCCCC---------------C------------------------
Q 003463          215 RRRKLDIHFS-----------------------IPKDNPS---------------D------------------------  232 (818)
Q Consensus       215 ~gr~L~V~~a-----------------------~pk~~~~---------------~------------------------  232 (818)
                      ..+-|.|-.+                       .+.....               .                        
T Consensus       170 GhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~g  249 (510)
T KOG4211|consen  170 GHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFG  249 (510)
T ss_pred             ccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccc
Confidence            5444433211                       0000000               0                        


Q ss_pred             -----CC---------------------CC-ccceeeecCCCCCCHHHHHHHhhccCCe---EEEEecCCCCceEEEEEc
Q 003463          233 -----KD---------------------LN-QGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFY  282 (818)
Q Consensus       233 -----~~---------------------~~-~~tL~V~NLp~~vteedL~~lFs~fG~I---~~vr~~g~srG~aFVeF~  282 (818)
                           ++                     .. ...++.++||+..++.+|..+|+..-.+   .+|..+++..|-|+|+|.
T Consensus       250 s~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~  329 (510)
T KOG4211|consen  250 SYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFA  329 (510)
T ss_pred             ccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecc
Confidence                 00                     00 0257788999999999999999976443   233346777889999999


Q ss_pred             CHHHHHHHHHHcCCCccCCceEEE
Q 003463          283 DVRAAEAALKSLNRSDIAGKRIKL  306 (818)
Q Consensus       283 d~e~A~~Ai~~LnG~~i~Gr~L~V  306 (818)
                      +.++|..|+. -++..+..+-|.+
T Consensus       330 t~edav~Ams-kd~anm~hrYVEl  352 (510)
T KOG4211|consen  330 TGEDAVGAMG-KDGANMGHRYVEL  352 (510)
T ss_pred             cchhhHhhhc-cCCcccCcceeee
Confidence            9999999997 3666666655554

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.17  E-value=3.4e-11  Score=117.75  Aligned_cols=77  Identities=26%  Similarity=0.516  Sum_probs=73.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      .++|||+||+.++++.||..+|..||.|..|.+.....|||||+|++..+|+.|+..|+|..|.|..|.|+++.-..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            68999999999999999999999999999999988999999999999999999999999999999999999886443

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.17  E-value=1.8e-10  Score=119.80  Aligned_cols=119  Identities=27%  Similarity=0.444  Sum_probs=101.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC-
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI-  225 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~-  225 (818)
                      .++|||+|||.++++++|+++|.+||.|..+.+     +++.+|||||.|.+.++|..|++.+++..|.|+.|.|.+.. 
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            699999999999999999999999999977762     57899999999999999999999999999999999999954 


Q ss_pred             ---CCCCCC----------------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec
Q 003463          226 ---PKDNPS----------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET  270 (818)
Q Consensus       226 ---pk~~~~----------------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~  270 (818)
                         ++....                ........+++.+++..++..++...|..+|.+..+.+.
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLP  258 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeecc
Confidence               222111                011123579999999999999999999999999777653

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=3.3e-10  Score=101.93  Aligned_cols=81  Identities=23%  Similarity=0.407  Sum_probs=73.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      -...|||.|||+++|.|+..++|.+||.|..||+  +...+|.|||-|++..+|.+|+..|+|..+.++.|.|-|..+..
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            3468999999999999999999999999999997  45568999999999999999999999999999999999988766


Q ss_pred             ccc
Q 003463          314 ARR  316 (818)
Q Consensus       314 ~r~  316 (818)
                      ..+
T Consensus        97 ~~~   99 (124)
T KOG0114|consen   97 AFK   99 (124)
T ss_pred             HHH
Confidence            444

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.13  E-value=6.8e-11  Score=110.07  Aligned_cols=75  Identities=27%  Similarity=0.494  Sum_probs=69.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..++||||+||+..++||+|.+||+++|+|+.|.+     +....|||||+|.+.++|+.|++.+++..+..++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            46899999999999999999999999999999873     4557899999999999999999999999999999999875

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.13  E-value=1.2e-10  Score=119.29  Aligned_cols=77  Identities=25%  Similarity=0.428  Sum_probs=72.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|.|.||+.++++++|+++|.+||.|.+|.     .++.++|||||.|.++++|++||..|||.-++.-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            456899999999999999999999999999884     588999999999999999999999999999999999999999


Q ss_pred             CC
Q 003463          311 PG  312 (818)
Q Consensus       311 ~~  312 (818)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=1.4e-10  Score=122.78  Aligned_cols=99  Identities=18%  Similarity=0.295  Sum_probs=80.3

Q ss_pred             cCcccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe---cCCCCceEEEEEcCHHH
Q 003463          210 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRA  286 (818)
Q Consensus       210 ng~~l~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~---~g~srG~aFVeF~d~e~  286 (818)
                      ++....|..+.+..+..    +......++|+|+|||+...+-||+.+|.+||+|.+|.|   ...+|||+||+|++.+|
T Consensus        73 ~~~~t~g~~~~~~~st~----s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~d  148 (376)
T KOG0125|consen   73 NGAPTDGQPIQTQPSTN----SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPAD  148 (376)
T ss_pred             CCCCCCCCccccCCCCc----CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhh
Confidence            44555566655543322    122224568999999999999999999999999999875   34579999999999999


Q ss_pred             HHHHHHHcCCCccCCceEEEEecCCC
Q 003463          287 AEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       287 A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      |++|..+|||..+.||+|.|..+..+
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchh
Confidence            99999999999999999999988654

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.12  E-value=6.2e-10  Score=119.30  Aligned_cols=172  Identities=20%  Similarity=0.309  Sum_probs=135.4

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHh--cCccccccccc
Q 003463          143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLD  220 (818)
Q Consensus       143 g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~L--ng~~l~gr~L~  220 (818)
                      +..+....++-.|.|++|-..++|.+|.+.++.||.|..+.. ...+..|.|+|+|++.|++++..-  +...+.|+.--
T Consensus        22 ~~dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~-~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   22 NADPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTC-MPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEe-ccccceeeeeeccccchhhheehhccCcccccCchhh
Confidence            344555667889999999999999999999999999998854 445678999999999999998632  34556788777


Q ss_pred             ccccCCCCCCCCCC---CCcccee--eecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcC
Q 003463          221 IHFSIPKDNPSDKD---LNQGTLV--VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       221 V~~a~pk~~~~~~~---~~~~tL~--V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      +.|+..+......+   ...+.|.  |-|--+.+|.+-|..++.+.|+|.+|-+..+..-.|.|||++.+.|++|..+||
T Consensus       101 ~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alN  180 (494)
T KOG1456|consen  101 FNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALN  180 (494)
T ss_pred             cccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcc
Confidence            77775443322111   1223344  445557899999999999999999998876655579999999999999999999


Q ss_pred             CCccC-C-ceEEEEecCCCccc
Q 003463          296 RSDIA-G-KRIKLEPSRPGGAR  315 (818)
Q Consensus       296 G~~i~-G-r~L~V~~a~~~~~r  315 (818)
                      |..|. | ++|+|+||+|..-+
T Consensus       181 GADIYsGCCTLKIeyAkP~rln  202 (494)
T KOG1456|consen  181 GADIYSGCCTLKIEYAKPTRLN  202 (494)
T ss_pred             cccccccceeEEEEecCcceee
Confidence            99886 4 78999999997643

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.12  E-value=7.4e-11  Score=132.62  Aligned_cols=162  Identities=27%  Similarity=0.408  Sum_probs=131.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|+|-|||..|++++|+.+|+.||+|+.|+.+...+|.+||+|+|.++|++|+++|++.++.|+.|+........
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~~  151 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARRA  151 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccccc
Confidence            56789999999999999999999999999999999888899999999999999999999999999999988833221110


Q ss_pred             C------------------CCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHH
Q 003463          229 N------------------PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAA  290 (818)
Q Consensus       229 ~------------------~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~A  290 (818)
                      .                  .....-....+++- |++..+..-++.+|+.+|.+.. +.++..+..-|++|.+..++..+
T Consensus       152 ~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~~  229 (549)
T KOG4660|consen  152 MGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAFS  229 (549)
T ss_pred             chhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhhc
Confidence            0                  00011122345544 9999998888889999999988 88888777899999999999777


Q ss_pred             HHHcCCCccCCceEEEEecCCCc
Q 003463          291 LKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       291 i~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      .... |..+.+....+.++.+.+
T Consensus       230 ~~~~-G~~~s~~~~v~t~S~~~g  251 (549)
T KOG4660|consen  230 EPRG-GFLISNSSGVITFSGPGG  251 (549)
T ss_pred             ccCC-ceecCCCCceEEecCCCc
Confidence            7744 777788888888887744

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.10  E-value=2.6e-10  Score=119.98  Aligned_cols=74  Identities=20%  Similarity=0.413  Sum_probs=67.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecC--CCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP--HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g--~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      .++|||+||++.+|+++|+++|+.||+|++|++..  ..+|||||+|.+.++|+.|+. |+|..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            45899999999999999999999999999998743  357999999999999999996 999999999999999764

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=1.4e-10  Score=107.97  Aligned_cols=76  Identities=21%  Similarity=0.345  Sum_probs=69.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...||||+||...++||+|.++|+++|+|+.|-     .+....|||||+|...++|+.|++-++|..++.+.|+|.|.-
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            456999999999999999999999999999983     455678999999999999999999999999999999999864


Q ss_pred             C
Q 003463          311 P  311 (818)
Q Consensus       311 ~  311 (818)
                      .
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            3

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.09  E-value=3.4e-10  Score=101.88  Aligned_cols=80  Identities=29%  Similarity=0.490  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ...++.|||+|||.++|.|++.++|.+||.|+.|++  +...+|.|||.|+++.+|++|++.|.|..+.++.|.|.|..+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            345789999999999999999999999999999995  556799999999999999999999999999999999998876


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      .+
T Consensus        95 ~~   96 (124)
T KOG0114|consen   95 ED   96 (124)
T ss_pred             HH
Confidence            43

>smart00362 RRM_2 RNA recognition motif

Probab=99.07  E-value=5.6e-10  Score=92.62  Aligned_cols=69  Identities=32%  Similarity=0.643  Sum_probs=63.0

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEecCC---CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH---KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~---srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      +|+|+|||..+++++|+++|++||.|..+++...   .+++|||+|.+.++|.+|++.+++..+.|++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5899999999999999999999999999876433   47999999999999999999999999999999874

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.07  E-value=3.2e-10  Score=96.20  Aligned_cols=66  Identities=35%  Similarity=0.644  Sum_probs=58.6

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCeEEEEecCC----CCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH----KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       240 L~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~----srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      |||+|||+.+++++|+++|+.||.|..+++...    .+++|||+|.+.++|.+|++.+++..+.|++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999976433    478999999999999999999999999999885

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.06  E-value=2.9e-10  Score=120.47  Aligned_cols=79  Identities=23%  Similarity=0.400  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ...++|+|.|||....|-||+.+|++||+|.+|.+   .+-+|||+||+|++.+||++|.++|+|..+.||+|.|..+.+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            34579999999999999999999999999999874   566899999999999999999999999999999999998876


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      +-
T Consensus       174 rV  175 (376)
T KOG0125|consen  174 RV  175 (376)
T ss_pred             hh
Confidence            53

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.06  E-value=4.7e-10  Score=118.03  Aligned_cols=75  Identities=19%  Similarity=0.293  Sum_probs=68.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      .++|||+|||+.+||++|+++|+.||+|.+|.+  .+..+|||||+|.+.++|+.|+. |+|..|.|+.|.|..+...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            589999999999999999999999999999985  33368999999999999999996 9999999999999987643

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.06  E-value=4.8e-10  Score=114.82  Aligned_cols=79  Identities=22%  Similarity=0.430  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      .+...+|-|.||+.+++|++|++||.+||.|..|+     .++.++|||||.|.+.++|.+||+.|+|.-+..--|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            34678999999999999999999999999999987     4889999999999999999999999999999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9885

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.04  E-value=4.7e-10  Score=95.18  Aligned_cols=66  Identities=23%  Similarity=0.548  Sum_probs=58.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          155 LFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       155 LfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      |||+|||+++++++|+++|+.||.|..+..    .+..+|+|||+|.+.++|++|++.+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999998874    244689999999999999999999888999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.04  E-value=4.2e-10  Score=123.90  Aligned_cols=88  Identities=25%  Similarity=0.351  Sum_probs=73.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecC-CCCceEEEEEcCH--HHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP-HKRHHKFIEFYDV--RAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g-~srG~aFVeF~d~--e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ....+|||+||.+.++++||+.+|+.||.|.+|.+.. ..||||||+|.+.  .++.+||..|||.++.|+.|+|..|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            3446899999999999999999999999999986521 2289999999987  789999999999999999999999987


Q ss_pred             Ccccchhhhccchhcc
Q 003463          312 GGARRNLMLQLNQELE  327 (818)
Q Consensus       312 ~~~r~~~~~ql~~~~~  327 (818)
                      .     |+..|.+++.
T Consensus        88 ~-----YLeRLkrERe   98 (759)
T PLN03213         88 H-----YLARLKREWE   98 (759)
T ss_pred             H-----HHHHHHHHHH
Confidence            4     4555544433

>PF13893 RRM_5: RNA recognition motif

Probab=99.04  E-value=7.4e-10  Score=90.31  Aligned_cols=56  Identities=34%  Similarity=0.594  Sum_probs=51.6

Q ss_pred             HHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          254 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       254 L~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      |+++|++||+|+++.+....+++|||+|.+.++|.+|++.|||..+.|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999987666799999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.02  E-value=5.9e-10  Score=109.66  Aligned_cols=77  Identities=30%  Similarity=0.466  Sum_probs=70.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecC--CCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP--HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g--~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||.++.+.||.++|.+||.|..|.+..  ....||||+|++..+|+.||..-+|..++|++|+|+|++..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            457899999999999999999999999999997643  33579999999999999999999999999999999998765

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.99  E-value=6.6e-10  Score=113.51  Aligned_cols=76  Identities=22%  Similarity=0.421  Sum_probs=66.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      +..-++|||++|++.+..|+|+++|++||+|++..     .++++|||+||+|.|.++|.+|++. .+-.|+||+..+..
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            34457999999999999999999999999998876     3789999999999999999999984 45678899888877


Q ss_pred             cC
Q 003463          224 SI  225 (818)
Q Consensus       224 a~  225 (818)
                      +.
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            64

>smart00362 RRM_2 RNA recognition motif

Probab=98.97  E-value=1.9e-09  Score=89.42  Aligned_cols=69  Identities=30%  Similarity=0.580  Sum_probs=62.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      +|||+|||..+++++|+++|++||.|..+.+.   +..+|+|||+|.+.++|++|++.+++..+.|++|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999988743   3357999999999999999999999999999888763

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.96  E-value=6.4e-10  Score=111.20  Aligned_cols=76  Identities=33%  Similarity=0.543  Sum_probs=70.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..+|.|.||-+-++.++|+.+|++||.|-+|.|     +..++|||||.|.+..+|+.|+.+|+|..|+|+.|+|++|+-
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            458999999999999999999999999999854     778899999999999999999999999999999999998864


Q ss_pred             C
Q 003463          312 G  312 (818)
Q Consensus       312 ~  312 (818)
                      +
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            4

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.95  E-value=9.8e-10  Score=109.91  Aligned_cols=79  Identities=27%  Similarity=0.484  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      +.....+|.|-||-+-++.++|+.+|++||.|-+|++     +..++|||||.|.+..+|+.|+++|+|..|.|+.|.|+
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            3445689999999999999999999999999999984     78899999999999999999999999999999999999


Q ss_pred             ccCC
Q 003463          223 FSIP  226 (818)
Q Consensus       223 ~a~p  226 (818)
                      ++.-
T Consensus        89 ~ary   92 (256)
T KOG4207|consen   89 MARY   92 (256)
T ss_pred             hhhc
Confidence            8863

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.95  E-value=2.9e-09  Score=111.77  Aligned_cols=93  Identities=30%  Similarity=0.411  Sum_probs=80.2

Q ss_pred             cccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCC
Q 003463          222 HFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR  296 (818)
Q Consensus       222 ~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG  296 (818)
                      ....|..++......-+||||.-|+++++|.+|+..|+.||.|+.|+     ++++++|||||+|+++.+...|.+..+|
T Consensus        86 ~~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG  165 (335)
T KOG0113|consen   86 KLWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADG  165 (335)
T ss_pred             HhcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccC
Confidence            33455555444445567999999999999999999999999999985     5889999999999999999999999999


Q ss_pred             CccCCceEEEEecCCCcc
Q 003463          297 SDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       297 ~~i~Gr~L~V~~a~~~~~  314 (818)
                      ..|+|+.|.|.+-+....
T Consensus       166 ~~Idgrri~VDvERgRTv  183 (335)
T KOG0113|consen  166 IKIDGRRILVDVERGRTV  183 (335)
T ss_pred             ceecCcEEEEEecccccc
Confidence            999999999999775543

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.93  E-value=4.8e-09  Score=87.44  Aligned_cols=70  Identities=39%  Similarity=0.672  Sum_probs=64.0

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEecCC----CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH----KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~----srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      +|+|+|||..+++++|+++|+.||.|..+.+...    .+++|||+|.+.++|..|++.+++..+.|++|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999876443    378999999999999999999999999999999874

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.92  E-value=2.3e-09  Score=112.50  Aligned_cols=79  Identities=27%  Similarity=0.476  Sum_probs=73.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ...+|-+||||.-|+++++|.+|+..|+.||+|+.|.     ++++++|||||+|++..+...|.+..+|..|.|+.|-|
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~V  175 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILV  175 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEE
Confidence            3457889999999999999999999999999999987     58999999999999999999999999999999999998


Q ss_pred             cccC
Q 003463          222 HFSI  225 (818)
Q Consensus       222 ~~a~  225 (818)
                      .+-.
T Consensus       176 DvER  179 (335)
T KOG0113|consen  176 DVER  179 (335)
T ss_pred             Eecc
Confidence            8754

>smart00360 RRM RNA recognition motif

Probab=98.91  E-value=4.3e-09  Score=86.86  Aligned_cols=66  Identities=33%  Similarity=0.649  Sum_probs=59.6

Q ss_pred             eecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          242 VFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       242 V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      |+|||..+++++|+++|++||.|..+++.     +..+++|||+|.+.++|.+|++.|++..+.|++|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999998753     3447899999999999999999999999999999874

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.90  E-value=4.6e-09  Score=109.06  Aligned_cols=73  Identities=22%  Similarity=0.322  Sum_probs=66.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEec--CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~--g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..+|+|+||++.+|+++|+++|+.||+|.+|++.  +..+++|||+|.++++|+.|+. |+|..|.+++|.|....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            3589999999999999999999999999999863  3456899999999999999995 99999999999998764

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.89  E-value=1.1e-09  Score=110.38  Aligned_cols=81  Identities=27%  Similarity=0.505  Sum_probs=74.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||++|-.++++.-|...|=+||.|+.|.+     +.+.|||+||+|.-.|+|..||..||+.++.||.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4579999999999999999999999999999964     56789999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 003463          311 PGGARR  316 (818)
Q Consensus       311 ~~~~r~  316 (818)
                      |...+.
T Consensus        89 P~kike   94 (298)
T KOG0111|consen   89 PEKIKE   94 (298)
T ss_pred             CccccC
Confidence            976543

>PLN03213 repressor of silencing 3; Provisional

Probab=98.88  E-value=4e-09  Score=116.30  Aligned_cols=116  Identities=14%  Similarity=0.188  Sum_probs=84.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEEccH--HHHHHHHHHhcCcccccccccccccCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDI--RAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~d~--e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ....+|||+||++++++++|+.+|..||.|..|.+ ..+.||||||+|.+.  .++.+||..|+|..+.|+.|+|..+++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            34579999999999999999999999999999884 223499999999987  789999999999999999999998866


Q ss_pred             CCCC-------CCCCCCccceeeecCCCC-CCHHHHHHHhhccCCeEEEE
Q 003463          227 KDNP-------SDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIR  268 (818)
Q Consensus       227 k~~~-------~~~~~~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr  268 (818)
                      .-..       ........++.   |+.. .....|+-+|-+.++|+.+-
T Consensus        88 ~YLeRLkrEReea~s~~~~~~k---l~k~~~e~~qLnifFPrLrKvKslP  134 (759)
T PLN03213         88 HYLARLKREWEAASSTSDNTIK---APSDSPPATHLNIFFPRLRKVKAMP  134 (759)
T ss_pred             HHHHHHHHHHHHhhcccccccc---ccccCCccceeeEeccccccccccc
Confidence            3110       00001111221   2221 23345677777777777663

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.85  E-value=1.6e-09  Score=109.14  Aligned_cols=80  Identities=26%  Similarity=0.508  Sum_probs=75.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..|+|||++|..+|+|.-|...|-.||+|..|.+     +.++|||+||+|.-.|+|..||..|++.+|.||.|+|.++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4689999999999999999999999999999983     67899999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003463          226 PKDNP  230 (818)
Q Consensus       226 pk~~~  230 (818)
                      |.+..
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            87643

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.85  E-value=5.8e-09  Score=108.29  Aligned_cols=73  Identities=16%  Similarity=0.189  Sum_probs=66.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..+|||+||++.+|+++|+++|+.||+|.+|++  .++.+++|||+|++.++|+.|+. |+|..|.+++|.|....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            479999999999999999999999999999984  45667899999999999999996 99999999999987643

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.85  E-value=3.7e-09  Score=99.39  Aligned_cols=78  Identities=22%  Similarity=0.397  Sum_probs=70.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      .....|||.++....|+++|.+.|..||+|+.+.+     ++-.+|||+|+|++.++|++|+.+|||..+.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34458999999999999999999999999999954     5667999999999999999999999999999999999998


Q ss_pred             CCC
Q 003463          310 RPG  312 (818)
Q Consensus       310 ~~~  312 (818)
                      -.+
T Consensus       150 Fv~  152 (170)
T KOG0130|consen  150 FVK  152 (170)
T ss_pred             Eec
Confidence            543

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.83  E-value=1.2e-08  Score=85.11  Aligned_cols=70  Identities=34%  Similarity=0.652  Sum_probs=63.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCC----CcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~----ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      +|+|+|||..+++++|+++|+.||.|..+.+..    ..+|+|||+|.+.++|..|++.+++..+.|+++.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999987432    3489999999999999999999999999999988764

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>smart00360 RRM RNA recognition motif

Probab=98.83  E-value=8.5e-09  Score=85.05  Aligned_cols=66  Identities=32%  Similarity=0.584  Sum_probs=59.4

Q ss_pred             EcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          157 VRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       157 V~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      |+|||..+++++|+++|++||.|..+.+     +++++|+|||+|.+.++|.+|++.+++..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6799999999999999999999988874     34568999999999999999999999999999988763

>PF13893 RRM_5: RNA recognition motif

Probab=98.81  E-value=7.8e-09  Score=84.26  Aligned_cols=56  Identities=23%  Similarity=0.591  Sum_probs=50.7

Q ss_pred             HHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          169 LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       169 Lr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      |+++|++||+|..+.+..+.+++|||+|.+.++|++|++.|++..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999875555799999999999999999999999999999999875

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.80  E-value=2.6e-08  Score=103.55  Aligned_cols=75  Identities=36%  Similarity=0.625  Sum_probs=69.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..+|||+|||.++|+++|+++|..||.|..+++     ++..+|+|||+|.+.++|..|+..++|..+.|++|.|.++.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            589999999999999999999999999987753     567899999999999999999999999999999999999765

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=1e-08  Score=104.96  Aligned_cols=78  Identities=27%  Similarity=0.352  Sum_probs=67.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ..-.+|||+||++.++.|+|++.|++||+|++..     .++++|||+||+|.|.++|.+|++.- .-.|+||+..|.+|
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLA   88 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchh
Confidence            3446899999999999999999999999999874     47889999999999999999999843 45789999999887


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      .-+.
T Consensus        89 ~lg~   92 (247)
T KOG0149|consen   89 SLGG   92 (247)
T ss_pred             hhcC
Confidence            6644

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=1.1e-09  Score=107.77  Aligned_cols=75  Identities=23%  Similarity=0.422  Sum_probs=69.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...-|||+|||+++||.||..+|++||+|+.|.     -||+++||||+.|+|.++..-|+..|||..|.||.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            456799999999999999999999999999984     388999999999999999999999999999999999997653

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.73  E-value=6.6e-09  Score=122.05  Aligned_cols=159  Identities=21%  Similarity=0.365  Sum_probs=138.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC----CCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~----~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...++|||++||+..+++.+|+..|..+|.|..|.+.    +....|+||.|.+...+-.|...+.+..|..-.+++.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            3457899999999999999999999999999998753    334559999999999999999999999998777777777


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCC--c
Q 003463          225 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--K  302 (818)
Q Consensus       225 ~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G--r  302 (818)
                      .++.      .....+++++|...+....|...|..||.|..|.+. +..-||+|.|++...|..|...|.|..|+|  +
T Consensus       449 ~~ks------t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~-hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~  521 (975)
T KOG0112|consen  449 QPKS------TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR-HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPR  521 (975)
T ss_pred             cccc------ccceeeccCCCCCCChHHHHHHHhhccCcceeeecc-cCCcceeeecccCccchhhHHHHhcCcCCCCCc
Confidence            6532      345579999999999999999999999999999874 445699999999999999999999999997  8


Q ss_pred             eEEEEecCCCcc
Q 003463          303 RIKLEPSRPGGA  314 (818)
Q Consensus       303 ~L~V~~a~~~~~  314 (818)
                      +|+|.|+.+...
T Consensus       522 r~rvdla~~~~~  533 (975)
T KOG0112|consen  522 RLRVDLASPPGA  533 (975)
T ss_pred             ccccccccCCCC
Confidence            899999987654

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.73  E-value=2e-08  Score=113.63  Aligned_cols=78  Identities=28%  Similarity=0.420  Sum_probs=73.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..+||+|+|+++++++|..+|+..|.|.+++     .+++.+||||++|.+.++|.+|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            6899999999999999999999999999986     47889999999999999999999999999999999999999876


Q ss_pred             ccc
Q 003463          313 GAR  315 (818)
Q Consensus       313 ~~r  315 (818)
                      ..+
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            544

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.72  E-value=9.7e-08  Score=107.15  Aligned_cols=141  Identities=18%  Similarity=0.294  Sum_probs=103.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-------CCCccc---EEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-------ACKHRG---FVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-------~~ksrG---~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      .-+++|||++||++++|++|...|..||.+..-..       ....+|   |+|+.|+++..++.-+.+...   ...++
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~~  333 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGNY  333 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccce
Confidence            45789999999999999999999999998764321       112456   999999999999887765322   22222


Q ss_pred             cccccCCCCC-------------------CCCCCCCccceeeecCCCCCCHHHHHHHhh-ccCCeEEEEec-----CCCC
Q 003463          220 DIHFSIPKDN-------------------PSDKDLNQGTLVVFNLDPSVSNEDLRQIFG-AYGEVKEIRET-----PHKR  274 (818)
Q Consensus       220 ~V~~a~pk~~-------------------~~~~~~~~~tL~V~NLp~~vteedL~~lFs-~fG~I~~vr~~-----g~sr  274 (818)
                      .++.+.+...                   ....-...+||||++||.-++.++|..+|+ -||.|..+-|+     +-.+
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCC
Confidence            2222221111                   111112457999999999999999999999 69999887543     2368


Q ss_pred             ceEEEEEcCHHHHHHHHHH
Q 003463          275 HHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       275 G~aFVeF~d~e~A~~Ai~~  293 (818)
                      |-|-|.|.+..+-.+||.+
T Consensus       414 GaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcceeeecccHHHHHHHhh
Confidence            8999999999999999973

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.70  E-value=1.9e-08  Score=113.85  Aligned_cols=76  Identities=24%  Similarity=0.438  Sum_probs=71.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      +.|||+|||++++|++|..+|+..|.|.+++     .+++.+||||++|.+.++|+.|++.|+|..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            8999999999999999999999999999988     48899999999999999999999999999999999999998654


Q ss_pred             C
Q 003463          228 D  228 (818)
Q Consensus       228 ~  228 (818)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.67  E-value=3.7e-08  Score=100.60  Aligned_cols=75  Identities=28%  Similarity=0.576  Sum_probs=70.6

Q ss_pred             ceeeecCCCCCCHHHHHH----HhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          239 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~----lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ||||.||+..+..++|+.    +|++||+|.+|..  +++.+|.|||.|.+.+.|..|+++|+|..+.|+.++|.||+.+
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~   90 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSD   90 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCc
Confidence            999999999999999998    9999999999965  5678999999999999999999999999999999999999876


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        91 s   91 (221)
T KOG4206|consen   91 S   91 (221)
T ss_pred             c
Confidence            5

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.66  E-value=2.5e-08  Score=93.89  Aligned_cols=77  Identities=18%  Similarity=0.486  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..-.|||.++...++|++|.+.|..||+|+.+.     .++-.+|||+|+|.+.++|+.|+..+||..|.+++|.|.|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            345899999999999999999999999999987     367789999999999999999999999999999999999985


Q ss_pred             CC
Q 003463          226 PK  227 (818)
Q Consensus       226 pk  227 (818)
                      -+
T Consensus       151 v~  152 (170)
T KOG0130|consen  151 VK  152 (170)
T ss_pred             ec
Confidence            43

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.65  E-value=4.1e-08  Score=101.59  Aligned_cols=97  Identities=20%  Similarity=0.348  Sum_probs=81.7

Q ss_pred             cccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHH
Q 003463          216 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAAL  291 (818)
Q Consensus       216 gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai  291 (818)
                      .|+|.|+.+......    ..+++|||+-|.+.-.|||++.+|.+||.|.+|.+    ++.+||+|||.|.+..+|..||
T Consensus         2 nrpiqvkpadsesrg----~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI   77 (371)
T KOG0146|consen    2 NRPIQVKPADSESRG----GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAI   77 (371)
T ss_pred             CCCccccccccccCC----ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHH
Confidence            467788776654332    25678999999999999999999999999999965    5678999999999999999999


Q ss_pred             HHcCCC-ccCC--ceEEEEecCCCcccc
Q 003463          292 KSLNRS-DIAG--KRIKLEPSRPGGARR  316 (818)
Q Consensus       292 ~~LnG~-~i~G--r~L~V~~a~~~~~r~  316 (818)
                      ..|+|. .+.|  ..|.|+|+...++|.
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~  105 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERT  105 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHH
Confidence            999996 5555  789999998877664

>smart00361 RRM_1 RNA recognition motif

Probab=98.63  E-value=7.8e-08  Score=82.30  Aligned_cols=57  Identities=33%  Similarity=0.513  Sum_probs=50.5

Q ss_pred             HHHHHHHhh----ccCCeEEEE---e---c--CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          251 NEDLRQIFG----AYGEVKEIR---E---T--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       251 eedL~~lFs----~fG~I~~vr---~---~--g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      +++|+++|+    +||.|.+|.   +   +  +.++|+|||+|.+.++|.+|++.|||..+.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            678899998    999999874   2   2  6679999999999999999999999999999999863

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.62  E-value=4.8e-09  Score=103.22  Aligned_cols=75  Identities=20%  Similarity=0.435  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .+.-|||+|||++.||.||.-.|++||+|..|.     .+|+++||||+.|+|.++..-|+..|||..|.||.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            467899999999999999999999999999986     489999999999999999999999999999999999997653

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.57  E-value=1.3e-07  Score=107.94  Aligned_cols=161  Identities=20%  Similarity=0.354  Sum_probs=129.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcC-----------C-CEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQY-----------G-DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  218 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~f-----------G-~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~  218 (818)
                      ..+.++|+++|..++++.+..+|..-           | .|..+.+ +..+.|||++|.+.++|..|+. +++..+.|+.
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~-n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g~~  251 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL-NLEKNFAFIEFRSISEATEAMA-LDGIIFEGRP  251 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee-cccccceeEEecCCCchhhhhc-ccchhhCCCC
Confidence            35789999999999999999998743           3 2566654 5678999999999999999998 7888888887


Q ss_pred             ccccccCCCC-------------------CCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCC
Q 003463          219 LDIHFSIPKD-------------------NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKR  274 (818)
Q Consensus       219 L~V~~a~pk~-------------------~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~sr  274 (818)
                      +++.--....                   ...........++|++||..+++++++++...||.++..++     ++.++
T Consensus       252 ~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~sk  331 (500)
T KOG0120|consen  252 LKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSK  331 (500)
T ss_pred             ceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccccccccc
Confidence            7654211100                   00001112358999999999999999999999999887642     56789


Q ss_pred             ceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          275 HHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       275 G~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ||||.+|-+......|+..|||..+++++|.|..+-.+.
T Consensus       332 g~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  332 GFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             ceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            999999999999999999999999999999999987654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.56  E-value=1e-07  Score=110.63  Aligned_cols=107  Identities=28%  Similarity=0.408  Sum_probs=82.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS  231 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~  231 (818)
                      +|||||+.|+..++|.||.++|+.||+|.+|.+ ...+|+|||.+....+|++|+.+|.+..+.++.|+|.|+.-+.-..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~l-i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIIL-IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEee-ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            689999999999999999999999999999975 4479999999999999999999999999999999999997655332


Q ss_pred             C-CCCCccceeeecCCCCCCHHHHHHHhh
Q 003463          232 D-KDLNQGTLVVFNLDPSVSNEDLRQIFG  259 (818)
Q Consensus       232 ~-~~~~~~tL~V~NLp~~vteedL~~lFs  259 (818)
                      + ++.-+-.|=|.-||++.-.+||+.+++
T Consensus       500 e~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  500 EYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             hhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            1 111112233444565433333554443

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.55  E-value=1.3e-07  Score=109.82  Aligned_cols=79  Identities=29%  Similarity=0.410  Sum_probs=74.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcccc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  316 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r~  316 (818)
                      .+||||++|+..+++.||..+|+.||.|.+|.+. .+++||||.+..+.+|.+|+.+|+...+.++.|+|.|+..++-+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            3699999999999999999999999999999886 468899999999999999999999999999999999999888765

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.45  E-value=1.6e-07  Score=95.06  Aligned_cols=143  Identities=20%  Similarity=0.307  Sum_probs=115.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ...+||||.|+-..|+|+-|.++|-+-|+|..|.+    ..+.+ ||||.|.++-.+.-|++.++|..+.++.++|++-.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            34689999999999999999999999999999884    33344 99999999999999999999999999988887532


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  301 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G  301 (818)
                      -..        ..     -|+..++++.+...|+.-|.+..+|+    +++++.++|+.+....+.-.|+....+..+.-
T Consensus        86 G~s--------ha-----pld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~  152 (267)
T KOG4454|consen   86 GNS--------HA-----PLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQ  152 (267)
T ss_pred             CCC--------cc-----hhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCC
Confidence            111        00     16677899999999999999988865    45577899999988888888888777766655


Q ss_pred             ceEEE
Q 003463          302 KRIKL  306 (818)
Q Consensus       302 r~L~V  306 (818)
                      +++.+
T Consensus       153 ~~~~~  157 (267)
T KOG4454|consen  153 KKVTI  157 (267)
T ss_pred             CCccc
Confidence            55444

>smart00361 RRM_1 RNA recognition motif

Probab=98.44  E-value=3.7e-07  Score=78.14  Aligned_cols=56  Identities=20%  Similarity=0.374  Sum_probs=49.8

Q ss_pred             HHHHHHHhh----cCCCEEEEE---e---C--CCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          166 DSELRALFE----QYGDIRTLY---T---A--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       166 EeeLr~lFs----~fG~I~~v~---~---~--~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      +++|+++|+    +||.|.++.   +   +  +.++|||||+|.+.++|.+|++.|+|..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678888888    999999874   2   2  678999999999999999999999999999999875

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.41  E-value=4.8e-07  Score=97.16  Aligned_cols=87  Identities=23%  Similarity=0.440  Sum_probs=73.1

Q ss_pred             cccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHh-cCccccccc
Q 003463          140 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRK  218 (818)
Q Consensus       140 ~~~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~L-ng~~l~gr~  218 (818)
                      ...-..+..+...++|||++|-..++|.+|++.|.+||+|+++.+. ..+++|||+|.+.++|+.|.+++ +...|.|++
T Consensus       216 ~~~~lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~-~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  216 SAGTLEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRIL-PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             cccccCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEee-cccccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            3334455566677999999999999999999999999999999853 35679999999999999998864 556679999


Q ss_pred             ccccccCCC
Q 003463          219 LDIHFSIPK  227 (818)
Q Consensus       219 L~V~~a~pk  227 (818)
                      |+|.|..++
T Consensus       295 l~i~Wg~~~  303 (377)
T KOG0153|consen  295 LKIKWGRPK  303 (377)
T ss_pred             EEEEeCCCc
Confidence            999999883

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.40  E-value=6.5e-08  Score=113.57  Aligned_cols=139  Identities=14%  Similarity=0.229  Sum_probs=118.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      .++||+||+..+.+++|...|..+|.+..+.     ..++.+|+|||.|...+++.+|+....+..+.            
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g------------  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG------------  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh------------
Confidence            4789999999999999999999999877765     35778999999999999999999854443332            


Q ss_pred             CCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce
Q 003463          228 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  303 (818)
Q Consensus       228 ~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~  303 (818)
                               ...|+|.|+|+..|.++|+.++..+|.+++.++    .++.+|.|+|.|.+..+|.+++...++..+.-+.
T Consensus       736 ---------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~  806 (881)
T KOG0128|consen  736 ---------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENN  806 (881)
T ss_pred             ---------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcC
Confidence                     236899999999999999999999999999864    4677899999999999999999988888888777


Q ss_pred             EEEEecCCC
Q 003463          304 IKLEPSRPG  312 (818)
Q Consensus       304 L~V~~a~~~  312 (818)
                      +.|..+.|.
T Consensus       807 ~~v~vsnp~  815 (881)
T KOG0128|consen  807 GEVQVSNPE  815 (881)
T ss_pred             ccccccCCc
Confidence            777776553

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.33  E-value=1.2e-06  Score=94.33  Aligned_cols=78  Identities=35%  Similarity=0.509  Sum_probs=68.5

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc-CCCccCCceEEEEecCC
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L-nG~~i~Gr~L~V~~a~~  311 (818)
                      ++..-.+|||++|-..+++.+|++.|-+||+|+.|++... +++|||+|.+.++|+.|..++ |...|.|++|+|.|+++
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            4455679999999999999999999999999999998654 569999999999999988765 55688999999999988

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.28  E-value=1.2e-06  Score=90.42  Aligned_cols=143  Identities=17%  Similarity=0.302  Sum_probs=102.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhccccCcc----ccCCCC-----------
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHY----SVPNGA-----------  138 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~~~~~~----~l~n~~-----------  138 (818)
                      |.+++|++|++...+.++..+|..+|.+..     -....||+||.|.+.-.|...+..    .+....           
T Consensus         1 m~rv~vg~~~~~~~~~d~E~~f~~yg~~~d-----~~mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    1 MPRVYIGRLPYRARERDVERFFKGYGKIPD-----ADMKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             CCceeecccCCccchhHHHHHHhhcccccc-----ceeecccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            457899999999999999999999998721     112336677777766554422211    111000           


Q ss_pred             --ccc-cC----CCC---CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHH
Q 003463          139 --GTV-AG----EHP---YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA  208 (818)
Q Consensus       139 --~~~-~g----~~~---~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~  208 (818)
                        +.. .+    ...   ......+.|+|.+++..+.+.+|.+.|..+|.+.....   ..+++||+|...++|.+|+..
T Consensus        76 ~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~  152 (216)
T KOG0106|consen   76 GRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEK  152 (216)
T ss_pred             ccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchh
Confidence              000 01    000   11234568899999999999999999999999954432   678999999999999999999


Q ss_pred             hcCccccccccccccc
Q 003463          209 LQNKPLRRRKLDIHFS  224 (818)
Q Consensus       209 Lng~~l~gr~L~V~~a  224 (818)
                      |++..+.++.|.+...
T Consensus       153 l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  153 LDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccchhhcCceeeeccc
Confidence            9999999999999543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.26  E-value=1.2e-06  Score=95.02  Aligned_cols=163  Identities=20%  Similarity=0.290  Sum_probs=128.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...+++|++++...+.+.++..++..+|.+....     -...++|++.|.|...+.+..|+.......+.++.+.....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            3468999999999999999999999999766554     34568999999999999999999954444555555444333


Q ss_pred             CCCCC-------CCCCCCCcccee-eecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHH
Q 003463          225 IPKDN-------PSDKDLNQGTLV-VFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAAL  291 (818)
Q Consensus       225 ~pk~~-------~~~~~~~~~tL~-V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai  291 (818)
                      .....       ..... ...+++ |.+|+..+++++|+..|..+|.|..+++     ++..+++|+|+|.+..++..|+
T Consensus       166 ~~~~~~~~n~~~~~~~~-~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~  244 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSG-PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLAL  244 (285)
T ss_pred             ccccccccchhcccccC-ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHh
Confidence            22221       11111 223555 9999999999999999999999999975     4567899999999999999999


Q ss_pred             HHcCCCccCCceEEEEecCCCcc
Q 003463          292 KSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       292 ~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      .. ....+.++.+.+.+..+...
T Consensus       245 ~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  245 ND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             hc-ccCcccCcccccccCCCCcc
Confidence            87 88899999999999887653

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.24  E-value=1.2e-06  Score=93.88  Aligned_cols=76  Identities=28%  Similarity=0.446  Sum_probs=69.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..+.|||--|.+-+|++||.-+|+.||+|+.|.+     ++.+-.||||+|++.+++++|.-+|++..|..++|.|.|+.
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            4568999999999999999999999999999854     56677899999999999999999999999999999999986


Q ss_pred             C
Q 003463          311 P  311 (818)
Q Consensus       311 ~  311 (818)
                      .
T Consensus       318 S  318 (479)
T KOG0415|consen  318 S  318 (479)
T ss_pred             h
Confidence            4

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.20  E-value=1.3e-06  Score=90.56  Aligned_cols=129  Identities=17%  Similarity=0.181  Sum_probs=101.9

Q ss_pred             CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCC--CCCCCccceeeecCCCCCCHHHHHHHhhccC
Q 003463          185 ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS--DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG  262 (818)
Q Consensus       185 ~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~--~~~~~~~tL~V~NLp~~vteedL~~lFs~fG  262 (818)
                      .+..++++|+.|.....-.++-..-+++.+.-+.+++.-.....++.  +.+.++-+||.+.|..+++++-|...|.+|-
T Consensus       136 p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfp  215 (290)
T KOG0226|consen  136 PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFP  215 (290)
T ss_pred             CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecccccccccHHHHHHHHHhcc
Confidence            46678999999999888888877667777776666654443333322  3345567899999999999999999999985


Q ss_pred             Ce-----EEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          263 EV-----KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       263 ~I-----~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..     ..-+-+++++||+||.|.+..++..|+++|+|+.++.+.|++.-+..+.
T Consensus       216 sf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  216 SFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             chhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            33     2224578999999999999999999999999999999999987766554

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.15  E-value=5.3e-06  Score=83.86  Aligned_cols=79  Identities=18%  Similarity=0.265  Sum_probs=71.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhcc-CCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAY-GEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~f-G~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      ....+.++|..+|.-+.+.+|..+|.+| |.|..+|+     ||+++|||||+|++.+.|+-|-+.||+..+.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445689999999999999999999998 77777765     88999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 003463          308 PSRPG  312 (818)
Q Consensus       308 ~a~~~  312 (818)
                      +-.|.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            98776

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.13  E-value=2.3e-06  Score=91.84  Aligned_cols=77  Identities=21%  Similarity=0.419  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .|...|||..|.+-+|+++|.-+|+.||.|.+|.+     ++.+.-||||+|++.+++++|.-+|++..|..+.|.|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            46789999999999999999999999999999873     6778889999999999999999999999999999999998


Q ss_pred             CC
Q 003463          225 IP  226 (818)
Q Consensus       225 ~p  226 (818)
                      ..
T Consensus       317 QS  318 (479)
T KOG0415|consen  317 QS  318 (479)
T ss_pred             hh
Confidence            64

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.09  E-value=2.5e-05  Score=84.25  Aligned_cols=154  Identities=14%  Similarity=0.198  Sum_probs=105.2

Q ss_pred             cCccccccccCCCCCChHHHHHhhcCCCcEE---------Ee-ecCCCCCcccEEEEEecChhh---cc------ccCcc
Q 003463           72 GIMDDFDLRGLPSSLEDLEDYDIFGSGGGME---------LE-GEPQESLSMSMSKISISDSAS---GN------GLLHY  132 (818)
Q Consensus        72 ~v~~e~~V~~Lp~s~~E~el~diF~~~G~i~---------V~-~d~~t~~skG~a~v~f~~~~~---a~------~~~~~  132 (818)
                      .+-+.+||.+||.+++..+..++|+.+|.|-         |. .....+.-+|=+.+.|...+.   |.      .+.+.
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            3567899999999999999999999999871         11 112236667766666664432   11      11111


Q ss_pred             ccC---------CC---Ccc-----------------ccC-----CCCCCCCCCcEEEEcCCCC----CCc-------HH
Q 003463          133 SVP---------NG---AGT-----------------VAG-----EHPYGEHPSRTLFVRNINS----NVE-------DS  167 (818)
Q Consensus       133 ~l~---------n~---~~~-----------------~~g-----~~~~~e~~srtLfV~NLP~----~vT-------Ee  167 (818)
                      .+.         +.   ..+                 ..+     ..+......++|.++|+=.    ..+       ++
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            110         00   000                 001     1123334567999999831    222       35


Q ss_pred             HHHHHhhcCCCEEEEEe-CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          168 ELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       168 eLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +|++-.++||.|+.|.+ .....|.+-|.|.+.++|..||+.|+|+.+.||.|......
T Consensus       292 dl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            67777899999999986 45678999999999999999999999999999999877654

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.07  E-value=6e-06  Score=92.99  Aligned_cols=74  Identities=24%  Similarity=0.466  Sum_probs=67.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ++|+|.+|...+...||+.||++||+|+-.++     ++..++|+||++.+.++|.++|..|+.++|.|+.|.|+.++.
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            58999999999999999999999999988764     344578999999999999999999999999999999998875

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.07  E-value=8.9e-06  Score=82.28  Aligned_cols=79  Identities=18%  Similarity=0.377  Sum_probs=70.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcC-CCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQY-GDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~f-G~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ......+||..+|.-+-+.+|..+|.+| |.|+.++     .+|.++|||||+|++.+.|+-|-+.||+..+.++-|.|+
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3456789999999999999999999998 6777766     488999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 003463          223 FSIPK  227 (818)
Q Consensus       223 ~a~pk  227 (818)
                      +-.|.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            87654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.02  E-value=4.5e-05  Score=86.16  Aligned_cols=142  Identities=17%  Similarity=0.191  Sum_probs=102.4

Q ss_pred             hhhhhcCccccccccCCCCCChHHHHHhhcCCCcEEEeecC-CC----CCccc---EEEEEecChhhcc--------ccC
Q 003463           67 DELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEP-QE----SLSMS---MSKISISDSASGN--------GLL  130 (818)
Q Consensus        67 ddl~~~v~~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~-~t----~~skG---~a~v~f~~~~~a~--------~~~  130 (818)
                      +.........+||++||++++|.++...|..||.+.|+-.- .+    .-.+|   |.|+-|.+.....        ...
T Consensus       252 ~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~  331 (520)
T KOG0129|consen  252 GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEG  331 (520)
T ss_pred             CCCccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhccc
Confidence            34555567899999999999999999999999999776541 11    12446   9999998755321        111


Q ss_pred             cccc-------CCCCcc----------ccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhh-cCCCEEEEEeC-----CC
Q 003463          131 HYSV-------PNGAGT----------VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFE-QYGDIRTLYTA-----CK  187 (818)
Q Consensus       131 ~~~l-------~n~~~~----------~~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs-~fG~I~~v~~~-----~k  187 (818)
                      .+.+       ......          ........-++.+||||++||.-++.++|..+|+ -||.|..+-+.     +-
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KY  411 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKY  411 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCC
Confidence            1111       111000          0112333456889999999999999999999999 89999887642     23


Q ss_pred             cccEEEEEEccHHHHHHHHHH
Q 003463          188 HRGFVMISYYDIRAARTAMRA  208 (818)
Q Consensus       188 srG~AFV~F~d~e~A~~Al~~  208 (818)
                      .+|-|-|+|.+..+-.+||.+
T Consensus       412 PkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  412 PKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCcceeeecccHHHHHHHhh
Confidence            689999999999999999984

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=97.97  E-value=5.3e-06  Score=83.98  Aligned_cols=90  Identities=21%  Similarity=0.368  Sum_probs=60.5

Q ss_pred             CcceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEee--eccc--ccceeEEEEEecCCcccHHHHHHHhcCCcccCCC
Q 003463          652 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP--IDFK--NKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN  727 (818)
Q Consensus       652 d~rTtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Ylp--~d~~--~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~  727 (818)
                      ..++.|.||++|..+|++.+++.|+......++|-|++  .+..  ..+-...|||||.+.+++..|.+.|+|+.|..-.
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            46789999999999999999998887666665566665  3222  3344567999999999999999999999998654


Q ss_pred             C-ccEEEEEeeeccc
Q 003463          728 S-EKVASLAYARIQG  741 (818)
Q Consensus       728 s-~k~~~~~~A~iQg  741 (818)
                      . .-++.|.||--|-
T Consensus        85 g~~~~~~VE~Apyqk   99 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQK   99 (176)
T ss_dssp             S-EEEEEEEE-SS--
T ss_pred             CCCcceeEEEcchhc
Confidence            3 4889999998764

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.96  E-value=2.2e-05  Score=80.01  Aligned_cols=78  Identities=21%  Similarity=0.287  Sum_probs=65.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEE--EecCCC----CceEEEEEcCHHHHHHHHHHcCCCccC---CceEEEE
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHK----RHHKFIEFYDVRAAEAALKSLNRSDIA---GKRIKLE  307 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~v--r~~g~s----rG~aFVeF~d~e~A~~Ai~~LnG~~i~---Gr~L~V~  307 (818)
                      -+||||.+||.++...||..+|..|---+.+  +.+.+.    +-+|||.|.+..+|..|+.+|||..|+   +..|+|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            4799999999999999999999998544443  444433    368999999999999999999999887   6899999


Q ss_pred             ecCCCcc
Q 003463          308 PSRPGGA  314 (818)
Q Consensus       308 ~a~~~~~  314 (818)
                      +++....
T Consensus       114 lAKSNtK  120 (284)
T KOG1457|consen  114 LAKSNTK  120 (284)
T ss_pred             ehhcCcc
Confidence            9987653

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.95  E-value=7.2e-05  Score=81.39  Aligned_cols=153  Identities=16%  Similarity=0.240  Sum_probs=110.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhc-----CCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQ-----YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~-----fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .+..|-.++||+.-++.+|..+|+-     -|.+......++..|.+.|.|.|.|.-+.|++. +...+.++.|.|..+.
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~  137 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKAT  137 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccC
Confidence            4556778999999999999999983     234444445677889999999999999999984 7777788888876554


Q ss_pred             CCCC---------CCC---CCCCccceeeecCCCCCCHHHHHHHhhcc----CCeEE---EEe-cCCCCceEEEEEcCHH
Q 003463          226 PKDN---------PSD---KDLNQGTLVVFNLDPSVSNEDLRQIFGAY----GEVKE---IRE-TPHKRHHKFIEFYDVR  285 (818)
Q Consensus       226 pk~~---------~~~---~~~~~~tL~V~NLp~~vteedL~~lFs~f----G~I~~---vr~-~g~srG~aFVeF~d~e  285 (818)
                      ..+-         ...   ...+.-.|.+++||+++++.|+.++|.+-    |.++.   |+- +++..|-|||.|..++
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee  217 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEE  217 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHH
Confidence            3321         000   11234467789999999999999999742    22223   332 6777899999999999


Q ss_pred             HHHHHHHHcCCCccCCceEE
Q 003463          286 AAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       286 ~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      +|..|+.+ |...++-|.|.
T Consensus       218 ~aq~aL~k-hrq~iGqRYIE  236 (508)
T KOG1365|consen  218 DAQFALRK-HRQNIGQRYIE  236 (508)
T ss_pred             HHHHHHHH-HHHHHhHHHHH
Confidence            99999984 44444434443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.91  E-value=1e-06  Score=96.29  Aligned_cols=151  Identities=19%  Similarity=0.334  Sum_probs=121.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCc-ccccccccccccCCCCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK-PLRRRKLDIHFSIPKDNPS  231 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~-~l~gr~L~V~~a~pk~~~~  231 (818)
                      ..||++||.+.++..+|..+|..-- +-.-...--..||+||.+.+...|.+|++.++|+ .+.|+.+.+..+.++... 
T Consensus         2 nklyignL~p~~~psdl~svfg~ak-~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr-   79 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAK-IPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR-   79 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcccc-CCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH-
Confidence            4689999999999999999997541 0000001124689999999999999999999885 588999999998876643 


Q ss_pred             CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCC--CceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          232 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       232 ~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~s--rG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                           .+.+-|.|+|+...++-|..+...||.|..|......  .-..-|+|...+.+..||.+|+|..+....++|.|-
T Consensus        80 -----srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   80 -----SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             -----hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence                 3458999999999999999999999999998643221  223457889999999999999999999999999885


Q ss_pred             C
Q 003463          310 R  310 (818)
Q Consensus       310 ~  310 (818)
                      -
T Consensus       155 P  155 (584)
T KOG2193|consen  155 P  155 (584)
T ss_pred             c
Confidence            3

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.90  E-value=2.1e-05  Score=93.42  Aligned_cols=152  Identities=20%  Similarity=0.265  Sum_probs=118.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE-EEeecCC-CCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQ-ESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPY  147 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i-~V~~d~~-t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~~  147 (818)
                      .+.+|+++|...+++.++..+|..+|.+ +|.++.. -++..+++|+.|....++.    .+....+.++..++.-..+ 
T Consensus       372 trTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~-  450 (975)
T KOG0112|consen  372 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP-  450 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccccc-
Confidence            5789999999999999999999999988 4766664 5677789999888665443    2222223233222221111 


Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccc--ccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~a~  225 (818)
                      ...+++.++|++|+.++....|...|..||.|+.|.. .+..-||+|.|.+...|+.|++.+.|..|.+  +.+.|.|+.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy-~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY-RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeec-ccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            4567899999999999999999999999999999864 4456799999999999999999999999975  668888875


Q ss_pred             CC
Q 003463          226 PK  227 (818)
Q Consensus       226 pk  227 (818)
                      +.
T Consensus       530 ~~  531 (975)
T KOG0112|consen  530 PP  531 (975)
T ss_pred             CC
Confidence            54

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.87  E-value=3.7e-05  Score=81.05  Aligned_cols=78  Identities=24%  Similarity=0.350  Sum_probs=69.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...+|+|.|||+.|+++||+++|..||.++.+-+    .+.+.|.|-|.|...++|.+|++.++|..++|+.|++....+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            4468999999999999999999999998887743    567789999999999999999999999999999999988765


Q ss_pred             Cc
Q 003463          312 GG  313 (818)
Q Consensus       312 ~~  313 (818)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            44

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.86  E-value=2.9e-05  Score=81.88  Aligned_cols=77  Identities=22%  Similarity=0.363  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .-..+|+|.|||+.|++++|+++|+.||.+..+-    ..+.+.|.|-|.|...++|+.|++.+++..+.|+.|++....
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            3447899999999999999999999999887765    367889999999999999999999999999999999888664


Q ss_pred             C
Q 003463          226 P  226 (818)
Q Consensus       226 p  226 (818)
                      +
T Consensus       161 ~  161 (243)
T KOG0533|consen  161 S  161 (243)
T ss_pred             C
Confidence            4

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.86  E-value=2.8e-05  Score=90.02  Aligned_cols=85  Identities=18%  Similarity=0.364  Sum_probs=73.3

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--------CCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--------ACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       143 g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--------~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                      |....+...+++|||+||++.++++.|...|..||+|.++++        ..+.+.++||.|.+..+|++|++.|+|..+
T Consensus       165 gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv  244 (877)
T KOG0151|consen  165 GSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV  244 (877)
T ss_pred             CcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee
Confidence            344444556789999999999999999999999999999984        234577999999999999999999999999


Q ss_pred             ccccccccccCCC
Q 003463          215 RRRKLDIHFSIPK  227 (818)
Q Consensus       215 ~gr~L~V~~a~pk  227 (818)
                      .+..+++.|+++-
T Consensus       245 ~~~e~K~gWgk~V  257 (877)
T KOG0151|consen  245 MEYEMKLGWGKAV  257 (877)
T ss_pred             eeeeeeecccccc
Confidence            9999999998543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.83  E-value=3.8e-05  Score=86.70  Aligned_cols=76  Identities=18%  Similarity=0.340  Sum_probs=66.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .-.++|||.+|...+...+|+.||++||+|.-.++     +.-.+.|+||++.+.++|.+||..|+...|.|+-|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34689999999999999999999999999987662     2234679999999999999999999999999999999875


Q ss_pred             C
Q 003463          225 I  225 (818)
Q Consensus       225 ~  225 (818)
                      +
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            3

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.83  E-value=2.3e-05  Score=90.75  Aligned_cols=78  Identities=29%  Similarity=0.414  Sum_probs=70.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec--------CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~--------g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      +...++|||+||++.++++.|...|..||.|..+++.        ...+.++||-|.+..+|++|++.|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            4456799999999999999999999999999999752        23467999999999999999999999999999999


Q ss_pred             EEecCC
Q 003463          306 LEPSRP  311 (818)
Q Consensus       306 V~~a~~  311 (818)
                      +.|+++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999864

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.69  E-value=4.3e-05  Score=86.50  Aligned_cols=74  Identities=24%  Similarity=0.413  Sum_probs=62.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..+|||+|||.++++++|+++|..||.|+...+     .++...||||+|++.++++.|+.+ +-..|.+++|.|+--.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            456999999999999999999999999988763     244448999999999999999996 57788899998875443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.69  E-value=6.3e-05  Score=85.20  Aligned_cols=75  Identities=27%  Similarity=0.493  Sum_probs=64.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      .+|||.|||.++++++|+++|..||.|+..++.     ++..+||||+|.+.+++..||.+ +-..+++++|.|+-.++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            469999999999999999999999999987542     22338999999999999999985 577899999999987764


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            4

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.61  E-value=0.00021  Score=62.84  Aligned_cols=69  Identities=26%  Similarity=0.332  Sum_probs=48.0

Q ss_pred             cceeeecCCCCCCHHH----HHHHhhccC-CeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          238 GTLVVFNLDPSVSNED----LRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       238 ~tL~V~NLp~~vteed----L~~lFs~fG-~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..|+|.|||.+.+...    |++++.-+| +|..|  .   .+.|+|.|.+.+.|++|.+.|+|..+.|++|.|.|...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~---~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S---GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e---CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            3689999999887655    556777775 77766  2   36799999999999999999999999999999999843

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.51  E-value=4e-05  Score=83.64  Aligned_cols=158  Identities=16%  Similarity=0.135  Sum_probs=116.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC--------CCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~--------~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..|-|.||.+.+|.++++.||...|+|..+.+.        ......|||.|.|...+..|.. |.+..+-++.|.|..+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            489999999999999999999999999988732        2245689999999999998877 7777766665554322


Q ss_pred             CCCCCC-----------------------------C--CCC---------------------CCccceeeecCCCCCCHH
Q 003463          225 IPKDNP-----------------------------S--DKD---------------------LNQGTLVVFNLDPSVSNE  252 (818)
Q Consensus       225 ~pk~~~-----------------------------~--~~~---------------------~~~~tL~V~NLp~~vtee  252 (818)
                      ...-.+                             .  ...                     .-..+++|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            100000                             0  000                     001479999999999999


Q ss_pred             HHHHHhhccCCeEEEEec-CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          253 DLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       253 dL~~lFs~fG~I~~vr~~-g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ++-+.|..+|.|...+.. +....+|.|+|........|+. ++|.++.-...++..-+|.
T Consensus       167 e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~kP~  226 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIKPH  226 (479)
T ss_pred             hhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcCcc
Confidence            999999999999988753 3345678899999999999997 6777776444444444443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.49  E-value=0.00011  Score=77.35  Aligned_cols=79  Identities=24%  Similarity=0.372  Sum_probs=69.2

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      +......+||+|++..+|.+++...|+.||.|..+.     ..++.+||+||+|.+.+.+++|++ |+|..|.|+.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            344567899999999999999999999999997553     456689999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 003463          308 PSRPG  312 (818)
Q Consensus       308 ~a~~~  312 (818)
                      +.+-.
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87643

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.48  E-value=0.00022  Score=82.56  Aligned_cols=160  Identities=15%  Similarity=0.066  Sum_probs=114.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcC-CCEEEE---EeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQY-GDIRTL---YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~f-G~I~~v---~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .++.+-+.+.+.+.++.+++++|... -.-..+   .+.+...|-++|.|....++++|++. +......|.+.|.....
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCc
Confidence            34455567999999999999999732 222222   24455589999999999999999983 55556666666543211


Q ss_pred             CCC-------------------------CC----------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEE-EEec
Q 003463          227 KDN-------------------------PS----------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRET  270 (818)
Q Consensus       227 k~~-------------------------~~----------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~-vr~~  270 (818)
                      ...                         +.          ........|||..||..+++.++.++|...-.|++ |.++
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence            000                         00          00011258999999999999999999998777776 6553


Q ss_pred             ----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          271 ----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       271 ----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                          ++.++.|||+|..++++.+|...-+...++-+.|+|.-...
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~  513 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIAD  513 (944)
T ss_pred             cCCcccccchhhheeccccccchhhhcccccccCceEEEeechhh
Confidence                34567899999999999999987777777789999976543

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.46  E-value=0.00042  Score=63.34  Aligned_cols=73  Identities=18%  Similarity=0.352  Sum_probs=58.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcC--CCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccc----cccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQY--GDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR----RRKLDI  221 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~f--G~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~----gr~L~V  221 (818)
                      +||.|+|||...|.++|.+++...  |...-++     .++.+.|||||.|.+.+.|.+..+.++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            699999999999999999988753  3333333     35678999999999999999999999998875    345566


Q ss_pred             cccC
Q 003463          222 HFSI  225 (818)
Q Consensus       222 ~~a~  225 (818)
                      .||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6664

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.44  E-value=0.00038  Score=61.30  Aligned_cols=68  Identities=21%  Similarity=0.400  Sum_probs=48.7

Q ss_pred             cEEEEcCCCCCCcHHHH----HHHhhcCC-CEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          153 RTLFVRNINSNVEDSEL----RALFEQYG-DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeL----r~lFs~fG-~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..|+|.|||.+.+...|    +.++..+| +|..|     ..+.|+|.|.+.+.|++|.+.|+|..+.|++|.|.|..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            46999999999887664    56666775 67776     35789999999999999999999999999999999974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.43  E-value=9e-05  Score=75.55  Aligned_cols=75  Identities=20%  Similarity=0.198  Sum_probs=66.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...||||.|+...++|+-|.++|-+-|.|.+|.+.    ++.+ ||||+|.++....-|++.+||..+.+..++|.+-..
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            45799999999999999999999999999999763    2334 999999999999999999999999999999988543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.34  E-value=0.00035  Score=75.97  Aligned_cols=172  Identities=16%  Similarity=0.194  Sum_probs=120.8

Q ss_pred             cccccccCCCCCchhhhhhcCccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc--
Q 003463           53 VMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN--  127 (818)
Q Consensus        53 ~~~~~IgnLlPddeddl~~~v~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~--  127 (818)
                      .-..+++++....+.+   +....++++.+-+..++.++..++...|..   .+.+......++++..+.|.....+.  
T Consensus        70 ~~~~~~~~~s~~~~~~---~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~  146 (285)
T KOG4210|consen   70 DGLSEEDSLSSKEELR---GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAA  146 (285)
T ss_pred             cchhhcccccCCcccc---cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHH
Confidence            4455666666643222   456789999999999998888888888754   33333456678899999998766332  


Q ss_pred             -ccCccccCC-C-----CccccCCC------CCCCCCCcEEE-EcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCc
Q 003463          128 -GLLHYSVPN-G-----AGTVAGEH------PYGEHPSRTLF-VRNINSNVEDSELRALFEQYGDIRTLYT-----ACKH  188 (818)
Q Consensus       128 -~~~~~~l~n-~-----~~~~~g~~------~~~e~~srtLf-V~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ks  188 (818)
                       .+....... .     .....+..      .....+..++| |++|+.++++++|+..|..+|.|..++.     ++..
T Consensus       147 l~~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~  226 (285)
T KOG4210|consen  147 LEESGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDS  226 (285)
T ss_pred             HHhhhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccch
Confidence             111110100 0     00001110      11222344565 9999999999999999999999999983     6778


Q ss_pred             ccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       189 rG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      +|||+|.|.+...+..|+.. +...+.++++.+.+..+..
T Consensus       227 kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  227 KGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             hhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            99999999999999999987 8889999999999887654

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.31  E-value=9.7e-05  Score=87.59  Aligned_cols=139  Identities=14%  Similarity=0.184  Sum_probs=112.5

Q ss_pred             ccccccCCCCCChHHHHHhhcCCCcEEE---eecCCCCCcccEEEEEecChhhccccCccccCCCCccccCCCCCCCCCC
Q 003463           76 DFDLRGLPSSLEDLEDYDIFGSGGGMEL---EGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPS  152 (818)
Q Consensus        76 e~~V~~Lp~s~~E~el~diF~~~G~i~V---~~d~~t~~skG~a~v~f~~~~~a~~~~~~~l~n~~~~~~g~~~~~e~~s  152 (818)
                      +.|+++|+..+.+.++.+.|..+|.|++   ..-..+++-+|++++.|...+.+...+.+...    .+.+        .
T Consensus       669 ~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~----~~~g--------K  736 (881)
T KOG0128|consen  669 KIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDS----CFFG--------K  736 (881)
T ss_pred             HHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhh----hhhh--------h
Confidence            4889999999999999999999998842   22335778889999999987765544333221    1111        5


Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..|+|+|.|+..|.++|+.++..+|.+.+++    ..++.+|.|+|.|.+..+|.+++...+...+..+.+.|..+.|
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            6899999999999999999999999998886    3678899999999999999999998888888877777777655

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.29  E-value=0.00023  Score=74.10  Aligned_cols=76  Identities=21%  Similarity=0.304  Sum_probs=66.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCE-----EEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I-----~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .-+||.+.|..+++++-|...|.+|-..     ..-+.+++++||+||.|.+..++..|+++++|..++.+.|++..+.-
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~w  269 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEW  269 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhH
Confidence            4589999999999999999999988643     22235899999999999999999999999999999999999886654


Q ss_pred             C
Q 003463          227 K  227 (818)
Q Consensus       227 k  227 (818)
                      +
T Consensus       270 k  270 (290)
T KOG0226|consen  270 K  270 (290)
T ss_pred             H
Confidence            3

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.19  E-value=0.00073  Score=62.78  Aligned_cols=70  Identities=29%  Similarity=0.448  Sum_probs=45.0

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCC-----ccCCceEEEEec
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-----DIAGKRIKLEPS  309 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~-----~i~Gr~L~V~~a  309 (818)
                      .|.|.+++..++.++|++.|+.||.|..|++.. ....|+|+|.+.++|++|+..+.-.     .+.+..++++.-
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~-G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL   77 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR-GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL   77 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--T-T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecC-CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence            578999999999999999999999999999864 3347999999999999999877543     566666666553

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.12  E-value=0.0005  Score=72.58  Aligned_cols=77  Identities=16%  Similarity=0.304  Sum_probs=67.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      .+.+.+.+||+|+...+|.+++...|+.||.|..+.     ..+..+||+||+|.+.+.+++|++ |++..|.++.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            345678999999999999999999999999997544     345689999999999999999999 99999999999987


Q ss_pred             ccC
Q 003463          223 FSI  225 (818)
Q Consensus       223 ~a~  225 (818)
                      +..
T Consensus       176 ~~r  178 (231)
T KOG4209|consen  176 LKR  178 (231)
T ss_pred             eee
Confidence            654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.03  E-value=0.0022  Score=69.06  Aligned_cols=76  Identities=22%  Similarity=0.451  Sum_probs=62.2

Q ss_pred             ccceeeecCCCCCCHHH----H--HHHhhccCCeEEEEecCCC------Cce--EEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          237 QGTLVVFNLDPSVSNED----L--RQIFGAYGEVKEIRETPHK------RHH--KFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       237 ~~tL~V~NLp~~vteed----L--~~lFs~fG~I~~vr~~g~s------rG~--aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      ..-+||-+|++.+-.|+    |  .++|.+||.|+.|.+..+.      .+.  .||.|.+.++|.+||.+.+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            44689999999987776    3  3789999999999664321      122  39999999999999999999999999


Q ss_pred             eEEEEecCCC
Q 003463          303 RIKLEPSRPG  312 (818)
Q Consensus       303 ~L~V~~a~~~  312 (818)
                      .|+..|...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999997643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.61  E-value=0.0027  Score=68.45  Aligned_cols=75  Identities=24%  Similarity=0.398  Sum_probs=61.9

Q ss_pred             CcEEEEcCCCCCCcHHHH------HHHhhcCCCEEEEEeCCCc------ccE--EEEEEccHHHHHHHHHHhcCcccccc
Q 003463          152 SRTLFVRNINSNVEDSEL------RALFEQYGDIRTLYTACKH------RGF--VMISYYDIRAARTAMRALQNKPLRRR  217 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeL------r~lFs~fG~I~~v~~~~ks------rG~--AFV~F~d~e~A~~Al~~Lng~~l~gr  217 (818)
                      ..-+||-+||+.+-.|+.      .++|.+||.|..|.+..+.      .+.  +||+|.+.|+|.+||.+.+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            456899999999888872      3789999999998753331      222  59999999999999999999999999


Q ss_pred             cccccccCC
Q 003463          218 KLDIHFSIP  226 (818)
Q Consensus       218 ~L~V~~a~p  226 (818)
                      .|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988754

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.52  E-value=0.0051  Score=56.62  Aligned_cols=72  Identities=21%  Similarity=0.369  Sum_probs=53.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEE------------ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce-
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR------------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-  303 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr------------~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~-  303 (818)
                      ..-|.|.+.|+. ....|.+.|++||+|.+..            -.....++.-|+|+++.+|.+||+ -||..+.|.. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456899999988 5577889999999998875            123446789999999999999998 6999999864 


Q ss_pred             EEEEecC
Q 003463          304 IKLEPSR  310 (818)
Q Consensus       304 L~V~~a~  310 (818)
                      +-|.+++
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4477764

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.44  E-value=0.0029  Score=69.23  Aligned_cols=78  Identities=24%  Similarity=0.329  Sum_probs=69.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEE-------------EecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v-------------r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      ...+|||-+||..+++++|.++|.++|.|+.=             +++...|+-|.|.|+|...|+.|+.-++++.+.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            34589999999999999999999999988653             24667789999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 003463          303 RIKLEPSRPGG  313 (818)
Q Consensus       303 ~L~V~~a~~~~  313 (818)
                      .|+|.++..+.
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99999887554

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.41  E-value=0.0066  Score=49.36  Aligned_cols=52  Identities=21%  Similarity=0.441  Sum_probs=43.2

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHH
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAAL  291 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai  291 (818)
                      +.|.|.|.+++.. +++...|..||+|..+.++ ......+|+|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            3578999998765 4566688899999999986 44578999999999999985

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.39  E-value=0.0033  Score=69.58  Aligned_cols=103  Identities=25%  Similarity=0.346  Sum_probs=79.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCC-ccCCceEEEEecCCCcccc
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-DIAGKRIKLEPSRPGGARR  316 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~-~i~Gr~L~V~~a~~~~~r~  316 (818)
                      ..||++||.+.++..||..+|... .+-.....--..||+||.+.|..-|.+|++.++|+ ++.|+++.|..+-++..+.
T Consensus         2 nklyignL~p~~~psdl~svfg~a-k~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrs   80 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDA-KIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRS   80 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccc-cCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHh
Confidence            368999999999999999999764 11100000123589999999999999999999997 8999999999998877653


Q ss_pred             --hhhhccchhccHHHHHHHHhhcCCC
Q 003463          317 --NLMLQLNQELEQDESRILQHQVGSP  341 (818)
Q Consensus       317 --~~~~ql~~~~~~~~l~~~f~~~GsP  341 (818)
                        ..+++..+++..+-+..+..+||.+
T Consensus        81 rk~Qirnippql~wevld~Ll~qyg~v  107 (584)
T KOG2193|consen   81 RKIQIRNIPPQLQWEVLDSLLAQYGTV  107 (584)
T ss_pred             hhhhHhcCCHHHHHHHHHHHHhccCCH
Confidence              4566777777777777777777755

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.35  E-value=0.0047  Score=68.74  Aligned_cols=66  Identities=33%  Similarity=0.473  Sum_probs=55.1

Q ss_pred             CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCC------------------CCceEEEEEcCHHHHHHHHHH
Q 003463          232 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH------------------KRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       232 ~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~------------------srG~aFVeF~d~e~A~~Ai~~  293 (818)
                      .++...++|.+.|||.+-.-+-|.+||+.+|.|+.||+..-                  .+-+|+|||+..+.|.+|.+.
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34456789999999999989999999999999999986321                  144699999999999999997


Q ss_pred             cCCC
Q 003463          294 LNRS  297 (818)
Q Consensus       294 LnG~  297 (818)
                      |+..
T Consensus       306 ~~~e  309 (484)
T KOG1855|consen  306 LNPE  309 (484)
T ss_pred             hchh
Confidence            7543

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=96.30  E-value=0.0089  Score=55.57  Aligned_cols=59  Identities=14%  Similarity=0.253  Sum_probs=39.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK  212 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~  212 (818)
                      ..|.|.+++..++-++|++.|+.||.|..|... +....|+|.|.+.++|+.|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~-~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS-RGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEec-CCCCEEEEEECCcchHHHHHHHHHhc
Confidence            468899999999999999999999999998753 34558999999999999999976544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.23  E-value=0.0075  Score=63.30  Aligned_cols=89  Identities=24%  Similarity=0.350  Sum_probs=74.3

Q ss_pred             HHHHHHHHhcCcccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEE----EecCCCCce
Q 003463          201 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHH  276 (818)
Q Consensus       201 ~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v----r~~g~srG~  276 (818)
                      -|+.|...|++....++.|+|.|+..           ..|||.||..-++.|.|.+.|+.||.|...    +..++..+-
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~-----------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~e   74 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH-----------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTRE   74 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc-----------ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccccccccc
Confidence            46677778999999999999999863           469999999999999999999999987653    445566678


Q ss_pred             EEEEEcCHHHHHHHHHHcCCCccC
Q 003463          277 KFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       277 aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      ++|+|...-.|.+|+..+.-.-+.
T Consensus        75 g~v~~~~k~~a~~a~rr~~~~g~~   98 (275)
T KOG0115|consen   75 GIVEFAKKPNARKAARRCREGGFG   98 (275)
T ss_pred             chhhhhcchhHHHHHHHhccCccc
Confidence            999999999999999987544333

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.18  E-value=0.011  Score=48.00  Aligned_cols=52  Identities=15%  Similarity=0.404  Sum_probs=43.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHH
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM  206 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al  206 (818)
                      +.|-|.+.+.+..+. +...|..||+|..+... ......+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            678899998876654 55588899999999865 45678999999999999985

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=96.18  E-value=0.0025  Score=70.34  Aligned_cols=73  Identities=19%  Similarity=0.402  Sum_probs=60.5

Q ss_pred             CcceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEee-eccccc-ceeEEEEEecCCcccHHHHHHHhcCCcccC
Q 003463          652 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP-IDFKNK-CNVGYAFINMLSPLHIIPFYEAFNGKKWEK  725 (818)
Q Consensus       652 d~rTtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Ylp-~d~~~~-~n~gyafin~~~~~~~~~f~~~f~g~~w~~  725 (818)
                      +....|.||++|+++|...|+..||- +...+.|.|+- -|+... |-.+.|||||..+.++..|...|+|+.+=.
T Consensus         5 ~~~~Kvv~rrlpp~l~~~~~~eqi~p-~~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~ifld   79 (376)
T KOG1295|consen    5 EAKVKVVVRRLPPKLTEEQLLEQINP-FPEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIFLD   79 (376)
T ss_pred             ccceeeeeecCCCcccHHHHhhhcCC-CccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEEec
Confidence            44578999999999999999999999 88888888765 554432 225569999999999999999999987754

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.16  E-value=0.011  Score=69.01  Aligned_cols=70  Identities=21%  Similarity=0.260  Sum_probs=60.5

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeE-EE--E--ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVK-EI--R--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~-~v--r--~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      .|-+.|+|++++-+||.++|..|-.+. +|  |  ..+...|-|.|-|++.++|.+|...|+++.|..+.|+|..
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            688999999999999999999995432 22  2  3566788999999999999999999999999999998864

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=95.62  E-value=0.012  Score=64.65  Aligned_cols=76  Identities=21%  Similarity=0.281  Sum_probs=67.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-------------eCCCcccEEEEEEccHHHHHHHHHHhcCcccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  217 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-------------~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr  217 (818)
                      ..-+|||-+||..+++.+|..+|.++|.|..-+             .+.+.||-|.|.|.|...|+.|+.-++++.+.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            356899999999999999999999999885533             3677899999999999999999999999999999


Q ss_pred             cccccccCC
Q 003463          218 KLDIHFSIP  226 (818)
Q Consensus       218 ~L~V~~a~p  226 (818)
                      +|+|.++..
T Consensus       145 ~ikvs~a~~  153 (351)
T KOG1995|consen  145 TIKVSLAER  153 (351)
T ss_pred             Cchhhhhhh
Confidence            999887753

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.56  E-value=0.0073  Score=63.36  Aligned_cols=68  Identities=29%  Similarity=0.523  Sum_probs=58.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCC-------------CCc----eEEEEEcCHHHHHHHHHHcCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-------------KRH----HKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~-------------srG----~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ..+.||+++||+.+....|+++|+.||.|-.|.+.+.             ++.    -|.|||.+...|......||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            5678999999999999999999999999999865321             111    27899999999999999999999


Q ss_pred             cCCce
Q 003463          299 IAGKR  303 (818)
Q Consensus       299 i~Gr~  303 (818)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99964

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.52  E-value=0.014  Score=65.17  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=59.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCC------------------cccEEEEEEccHHHHHHHHHHh
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------------------HRGFVMISYYDIRAARTAMRAL  209 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~k------------------srG~AFV~F~d~e~A~~Al~~L  209 (818)
                      .+-++++|.+-|||.+-.-+-|.++|..+|.|..|++...                  .+-+|+|+|+..+.|.+|.+.+
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3458999999999999999999999999999999984111                  2558999999999999999977


Q ss_pred             cCccccccccccc
Q 003463          210 QNKPLRRRKLDIH  222 (818)
Q Consensus       210 ng~~l~gr~L~V~  222 (818)
                      +...-...-|+|.
T Consensus       307 ~~e~~wr~glkvk  319 (484)
T KOG1855|consen  307 NPEQNWRMGLKVK  319 (484)
T ss_pred             chhhhhhhcchhh
Confidence            5544443344443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.37  E-value=0.026  Score=64.78  Aligned_cols=74  Identities=19%  Similarity=0.216  Sum_probs=57.6

Q ss_pred             CCccceeeecCCCC--CCH----HHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccC-Cce
Q 003463          235 LNQGTLVVFNLDPS--VSN----EDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKR  303 (818)
Q Consensus       235 ~~~~tL~V~NLp~~--vte----edL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~-Gr~  303 (818)
                      .-...|+|.|+|.-  ...    .-|.++|+++|+|....+    .+..+||.|++|.+.++|+.|++.|||+.|. .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            34568899999852  222    346688999999988743    4668999999999999999999999999887 466


Q ss_pred             EEEEe
Q 003463          304 IKLEP  308 (818)
Q Consensus       304 L~V~~  308 (818)
                      ..|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            66643

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=94.95  E-value=0.15  Score=47.86  Aligned_cols=86  Identities=19%  Similarity=0.293  Sum_probs=66.9

Q ss_pred             CcceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCcccCCCCccE
Q 003463          652 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKV  731 (818)
Q Consensus       652 d~rTtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~s~k~  731 (818)
                      ..+|+|-+=-+|+.++..+++..+-+.+.....-+.+.-|..  -|.-=+-|-|.+..+|..||+.|||++++..-. -+
T Consensus        10 ~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEp-E~   86 (110)
T PF07576_consen   10 ERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNSLEP-ET   86 (110)
T ss_pred             CCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCCCCC-ce
Confidence            344666666899999988777667677777777666666643  466669999999999999999999999988765 45


Q ss_pred             EEEEe-eecc
Q 003463          732 ASLAY-ARIQ  740 (818)
Q Consensus       732 ~~~~~-A~iQ  740 (818)
                      |.|.| .+||
T Consensus        87 ChvvfV~~Ve   96 (110)
T PF07576_consen   87 CHVVFVKSVE   96 (110)
T ss_pred             eEEEEEEEEE
Confidence            99999 4555

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.91  E-value=0.015  Score=61.14  Aligned_cols=62  Identities=31%  Similarity=0.399  Sum_probs=50.2

Q ss_pred             HHHHHHhh-ccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          252 EDLRQIFG-AYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       252 edL~~lFs-~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      +||...|+ +||+|+++.+.    ..-.|-++|.|...++|++|+..||+..+.|++|..+++.-..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            45555555 89999988542    2336779999999999999999999999999999999975433

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.79  E-value=0.09  Score=51.46  Aligned_cols=75  Identities=31%  Similarity=0.434  Sum_probs=53.8

Q ss_pred             CCccceeeecCCC------CCCH---HHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          235 LNQGTLVVFNLDP------SVSN---EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       235 ~~~~tL~V~NLp~------~vte---edL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      +...||.|.=+.+      ...+   .+|.+.|..||+|.=+|+.+   +.-.|.|.+-+.|.+|+. |+|.++.|+.|+
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~  100 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLK  100 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEE
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEE
Confidence            3456777775551      1221   37888899999999999875   468999999999999997 999999999999


Q ss_pred             EEecCCCc
Q 003463          306 LEPSRPGG  313 (818)
Q Consensus       306 V~~a~~~~  313 (818)
                      |+...|.-
T Consensus       101 i~LKtpdW  108 (146)
T PF08952_consen  101 IRLKTPDW  108 (146)
T ss_dssp             EEE-----
T ss_pred             EEeCCccH
Confidence            99977654

; PDB: 1UFW_A 2DNR_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=94.69  E-value=0.063  Score=49.51  Aligned_cols=72  Identities=11%  Similarity=0.186  Sum_probs=52.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE------------eCCCcccEEEEEEccHHHHHHHHHHhcCccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  218 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~------------~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~  218 (818)
                      ..+-|.|-+.|+. ....|.+.|++||+|.+..            ..........|+|.+..+|++||. .||..+.|.-
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            4567889899988 5567889999999998875            112356689999999999999999 5999998754


Q ss_pred             c-ccccc
Q 003463          219 L-DIHFS  224 (818)
Q Consensus       219 L-~V~~a  224 (818)
                      | -|.++
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            3 45555

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=94.51  E-value=0.025  Score=59.48  Aligned_cols=68  Identities=21%  Similarity=0.414  Sum_probs=58.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC-------------CCccc----EEEEEEccHHHHHHHHHHhcCcc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-------------CKHRG----FVMISYYDIRAARTAMRALQNKP  213 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~-------------~ksrG----~AFV~F~d~e~A~~Al~~Lng~~  213 (818)
                      .+-.||+.+||+.+.-.-|+++|+.||.|-.|+..             +..+.    -|.|+|.+...|..+...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            45689999999999999999999999999999831             11222    37899999999999999999999


Q ss_pred             ccccc
Q 003463          214 LRRRK  218 (818)
Q Consensus       214 l~gr~  218 (818)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.48  E-value=0.12  Score=58.30  Aligned_cols=81  Identities=30%  Similarity=0.349  Sum_probs=70.8

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCcccCCCCccEEE
Q 003463          654 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVAS  733 (818)
Q Consensus       654 rTtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~s~k~~~  733 (818)
                      -|+|-|=-||+.+|..+|+..+.....---|+--++ |  .--|.--+-|-|.+..+|..||+.|||+.++..-.+ +|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivR-d--~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Ch  149 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVR-D--GMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCH  149 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEee-c--CCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-cee
Confidence            589999999999999999999998888888888888 3  444555599999999999999999999999887766 999


Q ss_pred             EEeee
Q 003463          734 LAYAR  738 (818)
Q Consensus       734 ~~~A~  738 (818)
                      |-|+.
T Consensus       150 ll~V~  154 (493)
T KOG0804|consen  150 LLYVD  154 (493)
T ss_pred             EEEEE
Confidence            99964

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.26  E-value=0.087  Score=56.35  Aligned_cols=61  Identities=20%  Similarity=0.248  Sum_probs=49.7

Q ss_pred             HHHHHHHhhccCCeEEEEec---CCC---CceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          251 NEDLRQIFGAYGEVKEIRET---PHK---RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       251 eedL~~lFs~fG~I~~vr~~---g~s---rG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ++++++.+++||+|..|-+.   +..   .--.||+|...++|.+|+-.|||..|+|+.++..|..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            57788999999999987542   111   11379999999999999999999999999999888653

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.18  E-value=0.087  Score=60.71  Aligned_cols=71  Identities=20%  Similarity=0.368  Sum_probs=55.2

Q ss_pred             CcEEEEcCCCCCCc--H----HHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccc-ccccc
Q 003463          152 SRTLFVRNINSNVE--D----SELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLD  220 (818)
Q Consensus       152 srtLfV~NLP~~vT--E----eeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~-gr~L~  220 (818)
                      ...|+|-|+|.--.  .    .-|.++|+++|+|..+..    .+..+||.|++|.+.++|+.|++.|+|..|. .+++.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            45777888874322  1    236689999999988873    5679999999999999999999999998886 44554


Q ss_pred             cc
Q 003463          221 IH  222 (818)
Q Consensus       221 V~  222 (818)
                      |.
T Consensus       138 v~  139 (698)
T KOG2314|consen  138 VR  139 (698)
T ss_pred             ee
Confidence            43

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=93.51  E-value=0.062  Score=58.49  Aligned_cols=70  Identities=16%  Similarity=0.284  Sum_probs=57.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYG--DIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG--~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      .-.+||+||-+.+|++||.+.+...|  .+.+++     ..+.+||||+|...+..+.++.|+.|..+.|.|+.-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34799999999999999998887666  233333     57899999999999999999999999999898875444

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.24  E-value=0.27  Score=43.67  Aligned_cols=54  Identities=13%  Similarity=0.278  Sum_probs=42.1

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      ...+|. .|..+...||.++|++||.|.-.-+..   .-|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d---TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND---TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEECT---TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC---CcEEEEeecHHHHHHHHHHhc
Confidence            455666 999999999999999999987666653   459999999999999999876

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.98  E-value=0.39  Score=46.71  Aligned_cols=74  Identities=20%  Similarity=0.328  Sum_probs=57.0

Q ss_pred             CCCccceeeecCCCCC-CHHHHH---HHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          234 DLNQGTLVVFNLDPSV-SNEDLR---QIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~v-teedL~---~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +..-.||.|+=|...+ ..+||+   +..+.||.|.+|...|  +.-|.|.|.|..+|.+|+.++.. ...|..+.+.|.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            4455689998776665 334554   5567899999998876  45799999999999999999876 566788888875


Q ss_pred             C
Q 003463          310 R  310 (818)
Q Consensus       310 ~  310 (818)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            4

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=92.73  E-value=0.05  Score=57.37  Aligned_cols=58  Identities=22%  Similarity=0.351  Sum_probs=47.4

Q ss_pred             HHHHHHhh-cCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          167 SELRALFE-QYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       167 eeLr~lFs-~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      |+|...|+ +||+|+.+.+    .-.-.|-++|.|...++|++|+..|++..+.|++|...++
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34555555 8999998853    2235788999999999999999999999999999988765

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=92.66  E-value=0.12  Score=57.35  Aligned_cols=72  Identities=22%  Similarity=0.519  Sum_probs=59.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCC--------CceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~s--------rG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +.|.|.||.+.+|.+++..+|.-.|+|.++++.+.-        .-.|||.|.|...+..|.. |..+.+-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            478999999999999999999999999999875532        3469999999999988876 7777777777777654


Q ss_pred             C
Q 003463          310 R  310 (818)
Q Consensus       310 ~  310 (818)
                      -
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            3

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=92.32  E-value=0.11  Score=60.28  Aligned_cols=76  Identities=20%  Similarity=0.288  Sum_probs=62.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhc-cCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC---CceEEEEecCCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGA-YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA---GKRIKLEPSRPG  312 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~-fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~---Gr~L~V~~a~~~  312 (818)
                      .+.|+|.||-..+|.-+|+.++.. .|.|.+..+ .+-+.+|||.|.+.++|.+.+.+|||..+-   ++.|.+.|....
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~d  522 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRAD  522 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecchh
Confidence            468999999999999999999995 556666644 344678999999999999999999998653   589999998654


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus       523 e  523 (718)
T KOG2416|consen  523 E  523 (718)
T ss_pred             H
Confidence            3

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.74  E-value=0.33  Score=56.03  Aligned_cols=93  Identities=15%  Similarity=0.198  Sum_probs=65.9

Q ss_pred             HHHHHHhcCcccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhc--cCCeEEEEecCCCCceEEEE
Q 003463          203 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA--YGEVKEIRETPHKRHHKFIE  280 (818)
Q Consensus       203 ~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~--fG~I~~vr~~g~srG~aFVe  280 (818)
                      .++++...+..++.+-.+|..          ..+.+.|.|+-||..+.+|+++.||+.  +-++++|.+.-..  --||.
T Consensus       151 ~Evlresp~VqvDekgekVrp----------~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~--nWyIT  218 (684)
T KOG2591|consen  151 VEVLRESPNVQVDEKGEKVRP----------NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND--NWYIT  218 (684)
T ss_pred             HHHHhcCCCceeccCcccccc----------CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC--ceEEE
Confidence            344444444445544444432          224567889999999999999999985  6788888763222  36999


Q ss_pred             EcCHHHHHHHHHHcCC--CccCCceEEEE
Q 003463          281 FYDVRAAEAALKSLNR--SDIAGKRIKLE  307 (818)
Q Consensus       281 F~d~e~A~~Ai~~LnG--~~i~Gr~L~V~  307 (818)
                      |++..||+.|.+.|..  ++|.||+|...
T Consensus       219 fesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  219 FESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            9999999999998864  47778776544

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=91.64  E-value=0.8  Score=38.57  Aligned_cols=54  Identities=24%  Similarity=0.337  Sum_probs=41.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhcc----CCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAY----GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL  294 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~f----G~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L  294 (818)
                      ...|+|.|++ +++.+||+.+|..|    + ...|.-...  .-|-|-|.+.+.|.+|+.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdD--tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDD--TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecC--CcEEEEECCHHHHHHHHHcC
Confidence            3479999996 58889999999999    4 234432222  24889999999999999865

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.00  E-value=0.35  Score=55.89  Aligned_cols=79  Identities=18%  Similarity=0.209  Sum_probs=59.3

Q ss_pred             cCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhc--CCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcC--cccccc
Q 003463          142 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQ--YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRR  217 (818)
Q Consensus       142 ~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~--fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng--~~l~gr  217 (818)
                      .|++....+..+.|+++-||..+-+|+++.||+.  +-++.+|...-  ..--||+|++..||+.|.+.|..  +.|.|+
T Consensus       165 kgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~--N~nWyITfesd~DAQqAykylreevk~fqgK  242 (684)
T KOG2591|consen  165 KGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAH--NDNWYITFESDTDAQQAYKYLREEVKTFQGK  242 (684)
T ss_pred             CccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeee--cCceEEEeecchhHHHHHHHHHHHHHhhcCc
Confidence            4444444555678889999999999999999984  67788876321  22368999999999999998865  456777


Q ss_pred             ccccc
Q 003463          218 KLDIH  222 (818)
Q Consensus       218 ~L~V~  222 (818)
                      +|..+
T Consensus       243 pImAR  247 (684)
T KOG2591|consen  243 PIMAR  247 (684)
T ss_pred             chhhh
Confidence            66544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=90.92  E-value=1  Score=40.13  Aligned_cols=55  Identities=15%  Similarity=0.316  Sum_probs=42.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN  211 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng  211 (818)
                      ...+|. +|..+...||.++|+.||.|.--.+.   ..-|||...+.+.|..|+..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~---dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN---DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEEC---TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc---CCcEEEEeecHHHHHHHHHHhcc
Confidence            456666 99999999999999999998866553   45699999999999999997754

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=90.80  E-value=0.5  Score=46.38  Aligned_cols=73  Identities=25%  Similarity=0.371  Sum_probs=51.5

Q ss_pred             CCcEEEEcCCC-----CCCcH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          151 PSRTLFVRNIN-----SNVED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       151 ~srtLfV~NLP-----~~vTE----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      |..||.|.=+.     ...-+    .+|.+.|..||+|.-++..   .+.-.|+|.+.+.|.+|+. ++|..+.|+.|+|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv---~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i  101 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV---GDTMWVTFRDGQSALAALS-LDGIQVNGRTLKI  101 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE---TTCEEEEESSCHHHHHHHH-GCCSEETTEEEEE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe---CCeEEEEECccHHHHHHHc-cCCcEECCEEEEE
Confidence            45677776444     11223    3677889999998887642   3568999999999999999 8999999999999


Q ss_pred             cccCCC
Q 003463          222 HFSIPK  227 (818)
Q Consensus       222 ~~a~pk  227 (818)
                      +...|.
T Consensus       102 ~LKtpd  107 (146)
T PF08952_consen  102 RLKTPD  107 (146)
T ss_dssp             EE----
T ss_pred             EeCCcc
Confidence            876553

; PDB: 1UFW_A 2DNR_A.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=90.76  E-value=0.33  Score=55.20  Aligned_cols=73  Identities=21%  Similarity=0.239  Sum_probs=58.6

Q ss_pred             eeeecCCCCC-CHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          240 LVVFNLDPSV-SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       240 L~V~NLp~~v-teedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      |-+.-.+..+ +.++|...|.+||+|..|.+.-. .-.|.|+|.+..+|-+|-. ..+..|+++.|+|.|-.+...
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~~  448 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSPV  448 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc-hhhheeeeeccccccchhc-cccceecCceeEEEEecCCcc
Confidence            3344444444 67899999999999999987433 4579999999999988876 799999999999999988663

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=90.45  E-value=0.52  Score=48.28  Aligned_cols=63  Identities=17%  Similarity=0.275  Sum_probs=45.5

Q ss_pred             CHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcC--CCccCCceEEEEecCCCc
Q 003463          250 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       250 teedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~Ln--G~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+.|+++|..|+.+.....-+.- +-..|.|.+.++|.+|...|+  +..+.|..++|-|+.+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF-rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF-RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT-TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC-CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            457899999999988887654332 348999999999999999999  999999999999996544

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=89.88  E-value=1  Score=43.97  Aligned_cols=78  Identities=19%  Similarity=0.306  Sum_probs=57.8

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcH-HH---HHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          144 EHPYGEHPSRTLFVRNINSNVED-SE---LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       144 ~~~~~e~~srtLfV~NLP~~vTE-ee---Lr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      .+...+.|-.||.|+=|..++.. +|   +...++.||+|.+|...|  +--|.|.|+|..+|-+|+.+++. ...|..+
T Consensus        78 kk~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   78 KKNTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             cccCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            33445667889999877776543 34   445667899999996544  56799999999999999998876 5556666


Q ss_pred             ccccc
Q 003463          220 DIHFS  224 (818)
Q Consensus       220 ~V~~a  224 (818)
                      ++.|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            66654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=89.86  E-value=0.22  Score=57.82  Aligned_cols=67  Identities=21%  Similarity=0.344  Sum_probs=55.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhh-cCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFE-QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs-~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                      ....+++.|+|.||-.-.|.-+|+.++. ..|.|....+ .+-+..|||.|.+.++|.....+|+|..+
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~W  506 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQW  506 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhcccc
Confidence            3455788999999999999999999999 5666666643 34577899999999999999999998554

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=89.83  E-value=0.55  Score=50.44  Aligned_cols=74  Identities=18%  Similarity=0.344  Sum_probs=55.1

Q ss_pred             CcEEEEcCC--CCCCcH---HHHHHHhhcCCCEEEEEeC---C---CcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          152 SRTLFVRNI--NSNVED---SELRALFEQYGDIRTLYTA---C---KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       152 srtLfV~NL--P~~vTE---eeLr~lFs~fG~I~~v~~~---~---ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      ++.|.++|.  +-.+++   +++++.+++||.|..|.+.   +   ...--.||+|...++|.+|+-.|+|..+.|+.+.
T Consensus       281 tkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  281 TKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             hHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            344555554  233443   5788899999999988631   1   1123489999999999999999999999999988


Q ss_pred             ccccC
Q 003463          221 IHFSI  225 (818)
Q Consensus       221 V~~a~  225 (818)
                      ..|..
T Consensus       361 A~Fyn  365 (378)
T KOG1996|consen  361 ACFYN  365 (378)
T ss_pred             heecc
Confidence            87754

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=89.69  E-value=0.33  Score=53.09  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=60.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccC--CeEEE-----EecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG--~I~~v-----r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      .-++||+||-+.+|++||.+.....|  .+.++     |..+.+||||+|-..+..+.++.++.|-.++|.|..-.|...
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            34799999999999999999888766  23333     457889999999999999999999999999999966555443

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=89.06  E-value=1.5  Score=47.48  Aligned_cols=73  Identities=22%  Similarity=0.285  Sum_probs=57.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc-eEEEEecCCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIKLEPSRPG  312 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr-~L~V~~a~~~  312 (818)
                      +.=|-|.++++.- ..-|..+|++||.|.+.... .+..+-.|+|.++-+|.+||. -||+.|+|. -|-|+.+..+
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCH
Confidence            4457788998764 35678899999999887654 666799999999999999998 599999984 4556665544

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=87.69  E-value=0.32  Score=53.39  Aligned_cols=77  Identities=16%  Similarity=0.320  Sum_probs=60.5

Q ss_pred             ccceeeecCCCCCCHHHH-H--HHhhccCCeEEEEecCCC--------CceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          237 QGTLVVFNLDPSVSNEDL-R--QIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL-~--~lFs~fG~I~~vr~~g~s--------rG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      ..-+||-+|+..+..+++ +  +.|.+||.|..|......        ..-++|.|...++|..||...+|..++|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            346788889887755444 3  579999999998654321        12389999999999999999999999999999


Q ss_pred             EEecCCCc
Q 003463          306 LEPSRPGG  313 (818)
Q Consensus       306 V~~a~~~~  313 (818)
                      ..+...+-
T Consensus       157 a~~gttky  164 (327)
T KOG2068|consen  157 ASLGTTKY  164 (327)
T ss_pred             HhhCCCcc
Confidence            88877654

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=87.18  E-value=0.67  Score=47.14  Aligned_cols=77  Identities=8%  Similarity=0.060  Sum_probs=49.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhc-CCCE---EEEE--eC-----CCcccEEEEEEccHHHHHHHHHHhcCcccccc-
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQ-YGDI---RTLY--TA-----CKHRGFVMISYYDIRAARTAMRALQNKPLRRR-  217 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~-fG~I---~~v~--~~-----~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr-  217 (818)
                      ....+|.||+||+.+||+++.+.+.. +++-   ..+.  ..     .....-|||.|.+.+++...+..++|..+.+. 
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34569999999999999999998876 6665   3332  11     11233599999999999999999999877543 


Q ss_pred             ----cccccccCC
Q 003463          218 ----KLDIHFSIP  226 (818)
Q Consensus       218 ----~L~V~~a~p  226 (818)
                          ...|.+|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence                234555543

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=85.70  E-value=3.4  Score=34.89  Aligned_cols=53  Identities=21%  Similarity=0.431  Sum_probs=40.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcC----CCEEEEEeCCCcccEEEEEEccHHHHHHHHHHh
Q 003463          153 RTLFVRNINSNVEDSELRALFEQY----GDIRTLYTACKHRGFVMISYYDIRAARTAMRAL  209 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~f----G~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~L  209 (818)
                      .+|+|+++. +++.++|+.+|..|    ++.+--.+..   .-|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD---tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD---TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC---CcEEEEECCHHHHHHHHHcC
Confidence            579999985 58889999999999    5432212322   34789999999999999864

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=83.90  E-value=0.66  Score=50.97  Aligned_cols=76  Identities=20%  Similarity=0.305  Sum_probs=60.2

Q ss_pred             CcEEEEcCCCCCCcHHHHH---HHhhcCCCEEEEEeCCCc------cc--EEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          152 SRTLFVRNINSNVEDSELR---ALFEQYGDIRTLYTACKH------RG--FVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr---~lFs~fG~I~~v~~~~ks------rG--~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      .+-+||-+|+..+.++++.   +.|.+||.|..|.+.+..      .+  -++|+|...++|..||...+|..+.|+.++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            3567888999887766654   478899999998743321      11  389999999999999999999999999988


Q ss_pred             ccccCCC
Q 003463          221 IHFSIPK  227 (818)
Q Consensus       221 V~~a~pk  227 (818)
                      ..+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            8877654

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=82.56  E-value=1.9  Score=41.95  Aligned_cols=105  Identities=16%  Similarity=0.145  Sum_probs=73.0

Q ss_pred             CcHHHHHHHhh----cCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCCCCCC--c
Q 003463          164 VEDSELRALFE----QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN--Q  237 (818)
Q Consensus       164 vTEeeLr~lFs----~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~--~  237 (818)
                      .+-..|...+.    ..|.+.-..   -..++..+.|.+.++++++++ .....+.+..+.++.-.|..........  .
T Consensus        29 ~~~~~l~~~l~~~W~~~~~~~i~~---l~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~  104 (153)
T PF14111_consen   29 ISLSALEQELAKIWKLKGGVKIRD---LGDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEVKFEHIP  104 (153)
T ss_pred             CCHHHHHHHHHHHhCCCCcEEEEE---eCCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcccccccccceeccc
Confidence            44555555444    444444332   356899999999999999988 3556677888888766655444332222  2


Q ss_pred             cceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCC
Q 003463          238 GTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPH  272 (818)
Q Consensus       238 ~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~  272 (818)
                      -=|.|.|||.. .+++-|+++-+.+|++.+++....
T Consensus       105 vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~  140 (153)
T PF14111_consen  105 VWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTL  140 (153)
T ss_pred             hhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCC
Confidence            24678899987 588889999999999999986533

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=82.09  E-value=0.94  Score=54.87  Aligned_cols=73  Identities=16%  Similarity=0.251  Sum_probs=59.8

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC--CceEEEEecCCC
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA--GKRIKLEPSRPG  312 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~--Gr~L~V~~a~~~  312 (818)
                      +.++.|.+-..+-.-|..+|++||.|.+++.- +.-..|.|+|...+.|..|+.+|+|+++-  |-+.+|.+|+.-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtl-r~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTL-RDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheec-ccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            44555556677788899999999999999763 22457999999999999999999999764  788999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	818
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-05
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		4e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		8e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		8e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		2e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		2e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		3e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-04
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		6e-04
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		7e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		8e-04

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L N PL
Sbjct: 25  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 215 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 265
           R ++L + F+           +  +L V NL   VSNE L + F  +G+V+
Sbjct: 84  RGKQLRVRFAC----------HSASLTVRNLPQYVSNELLEEAFSVFGQVE 124

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/186 (22%), Positives = 87/186 (46%), Gaps = 28/186 (15%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 209
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+  +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 210 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 262
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 263 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIK-----------L 306
           ++K   +   P    HK   FIE+   ++++ A+ S+N  D+ G+ ++           L
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210
Query: 307 EPSRPG 312
            P+ PG
Sbjct: 211 TPATPG 216

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           LFV N+ +++ + + + LFE+YG+   ++   + RGF  I       A  A   L    L
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 215 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE----IRET 270
           + R L I F+           +   L V NL P VSNE L Q F  +G V++    + + 
Sbjct: 84  KSRPLRIRFAT----------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
Query: 271 PHKRHHKFIEFYDVRAAEAALKSLNR 296
                  F+EF    A   A K+L R
Sbjct: 134 GRATGKGFVEF---AAKPPARKALER 156

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 209
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+  +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 210 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 262
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 263 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           ++K   +   P    HK   FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 70/151 (46%), Gaps = 14/151 (9%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 209
           L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A++ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 210 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 266
               +R ++L + ++ P    S KD N   L V NL  +++++ L  IFG YG + +   
Sbjct: 66  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 267 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 295
           +R+  T   R   F+ +     A+ A+ +LN
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 155 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 207
           +FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 208 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 264
           AL N  +      +H  I   P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 78  ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 134
Query: 265 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 297
           +E R    P    R   F+ F     A+ A+K+++++
Sbjct: 135 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 171

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 155 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 207
           +FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 208 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 264
           AL N  +      +H  I   P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 66  ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 265 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 297
           +E R    P    R   F+ F     A+ A+K+++++
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 22/161 (13%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 205
           L V  +  N+   E R+LF   G+I +    CK           G+  ++Y D + A  A
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 265
           +  L    L+ + + + ++     PS   +    L V  L  +++ ++L Q+F  YG + 
Sbjct: 61  INTLNGLRLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 266 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 301
             R      T   R   FI F     AE A+K LN    +G
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 40/155 (25%), Positives = 64/155 (41%), Gaps = 22/155 (14%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 205
           L V  +  N+   E ++LF   GDI +    CK           G+  ++Y D   A  A
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIES----CKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 265
           +  L    L+ + + + ++     PS   +    L V  L  ++S +++ Q+F  YG + 
Sbjct: 63  INTLNGLKLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRII 118
Query: 266 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLN 295
             R      T   R   FI F     AE A+K LN
Sbjct: 119 TSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 14/151 (9%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 209
           L V  +  +  D EL ALF   G I T      Y      G+  + +     ++ A++ L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 210 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 266
               +R ++L + ++ P    S KD N   L V NL  +++++ L  IFG YG + +   
Sbjct: 77  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 267 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 295
           +R+  T   R   F+ +     A+ A+ +LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 41/186 (22%), Positives = 85/186 (45%), Gaps = 28/186 (15%)
Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 209
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+   
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 210 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQ-----GTLVVFNLDPSVSNEDLRQIFGAYG 262
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 263 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIK-----------L 306
           ++K   +   P    HK   FIE+   ++++ A+ S N  D+ G+ ++           L
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Query: 307 EPSRPG 312
            P+ PG
Sbjct: 195 TPATPG 200

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAA 290
           ++G L V  L    + + L Q+F  YG++ E+     RET   R   F+ F ++  A+ A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 291 LKSLNRSDIAGKRIKLEPS 309
           + ++N   + G++I+++ +
Sbjct: 71  MMAMNGKSVDGRQIRVDQA 89

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 150 HPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 203
            P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 204 TAMRALQNKPLRRRKLDIHFS 224
            A+R++Q  P   + + I ++
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/170 (26%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 155 LFVRNINSNVEDSELRA----LFEQYG----DIRTLYTACKHRGFVMISYYDIRAARTAM 206
           LFV N+N N    EL+     +F +      D+R   T    R F    Y D  +A    
Sbjct: 10  LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 207 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 266
           +AL+   L+    +I    PK   S K+ +  TL+  NL   V+ ++L+++F    E++ 
Sbjct: 63  KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 267 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL----EPSRPG 312
           + +    +   +IEF     AE   +    ++I G+ I L    EP   G
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPKGEG 172

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/160 (25%), Positives = 74/160 (46%), Gaps = 15/160 (9%)
Query: 155 LFVRNINSNVEDSELR-ALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 206
           LF+ N+N N   +EL+ A+ E +        D+RT      +R F    Y D  +A    
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 207 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 266
           +AL+   L+    +I    PK   S K     TL+  NL  +++ ++L+++F    E++ 
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 267 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           + +    +   +IEF     AE  L+    ++I G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/155 (21%), Positives = 74/155 (47%), Gaps = 12/155 (7%)
Query: 150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR------GFVMISYYDIRAAR 203
           +P  +L+V +++ +V ++ L   F   G I ++   C+        G+  +++     A 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 204 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 263
            A+  +    ++ + + I +S  + +PS +    G + + NLD S+ N+ L   F A+G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 264 V---KEIRETPHKRHHKFIEFYDVRAAEAALKSLN 295
           +   K + +    + + F+ F    AAE A++ +N
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 151 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 204
           P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 205 AMRALQNKPLRRRKLDIHFS 224
           A+R++Q  P   + + I ++
Sbjct: 68  ALRSMQGFPFYDKPMRIQYA 87

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRS 297
           TLV+ NL  S + E L+++F     +K  +    K + + FIEF     A+ AL S N+ 
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 298 DIAGKRIKLEPSRPGGA 314
           +I G+ I+LE   P G+
Sbjct: 77  EIEGRAIRLELQGPRGS 93

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/153 (23%), Positives = 67/153 (43%), Gaps = 11/153 (7%)
Query: 156 FVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMRA 208
           FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  A
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 209 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 268
           L N  +           P D+  +  +    L +  +    +  D+R  F ++G+++E R
Sbjct: 67  LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 269 --ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 297
               P    R   F+ F     A+ A+K+ +++
Sbjct: 127 ILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQA 159

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 151 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 204
           P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A  
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 205 AMRALQNKPLRRRKLDIHFS 224
           A+R++Q  P   + + I ++
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	818
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-32
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-32
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-29
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-29
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-26
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-24
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-25
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-24
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-04
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-21
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-21
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-20
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-20
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-19
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-15
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-19
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-11
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-11
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-14
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-14
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	9e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-11
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	7e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	9e-13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-08
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	8e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-12
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-12
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	7e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-09
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	3e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	8e-08
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	9e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-04
2div_A	99	TRNA selenocysteine associated protein; structural	1e-08
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-04
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-08
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-06
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-04
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	2e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	9e-04

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score =  124 bits (311), Expect = 2e-32
 Identities = 33/196 (16%), Positives = 59/196 (30%), Gaps = 39/196 (19%)

Query: 151 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 209
            S  L V  ++ S +    +  +F  YG++  +       G  M+   D  A   A+  L
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 210 QNKPLRRRKLDIHFS------------IPKDNPSDKDLNQG------------------- 238
            N  +  +K+++  S            +   + S KD ++                    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 239 --TLVVFNLDPSVSNEDLRQIFGAYG-----EVKEIRETPHKRHHKFIEFYDVRAAEAAL 291
              L  FN    V+ E+  +I    G      VK       +     +E+     A   L
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 292 KSLNRSDIAGKRIKLE 307
             LN   +        
Sbjct: 183 GFLNHYQMKNPNGPYP 198

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 69.3 bits (169), Expect = 1e-13
 Identities = 25/122 (20%), Positives = 46/122 (37%), Gaps = 1/122 (0%)

Query: 239 TLVVFNLDPSVSNED-LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
            L+V+ LD S  N D +  +F  YG V++++    K     +E  D  A + A+  LN +
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 298 DIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPI 357
            + G+++ +  S+           L       +                  N +Q  S +
Sbjct: 66  FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125

Query: 358 EH 359
            H
Sbjct: 126 LH 127

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 50.9 bits (121), Expect = 3e-07
 Identities = 9/82 (10%), Positives = 27/82 (32%), Gaps = 5/82 (6%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFVMISYYDIRAAR 203
           +HPS  L   N    V +     + ++ G      ++      +     ++ +     A 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 204 TAMRALQNKPLRRRKLDIHFSI 225
             +  L +  ++       +++
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTL 201

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score =  123 bits (309), Expect = 6e-32
 Identities = 49/226 (21%), Positives = 81/226 (35%), Gaps = 40/226 (17%)

Query: 126 GNGLLHYSVPNGAGTVAGEHPYGEHP------SRTLFVRNIN-SNVEDSELRALFEQYGD 178
           G+   H+   +G             P      +  L V N+N   V    L  LF  YGD
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 179 IRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS------IPKDNPSD 232
           ++ +      +   ++   D   A+ AM  L    L  + + I  S      +P++   D
Sbjct: 62  VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQED 121

Query: 233 KDLNQG-------------------------TLVVFNLDPSVSNEDLRQIFGAYGE-VKE 266
           + L +                          TL + N+ PSVS EDL+ +F + G  VK 
Sbjct: 122 QGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG 181

Query: 267 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRP 311
            +     R    I+   V  A  AL  L+  D+     +++  S+ 
Sbjct: 182 FKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 66.9 bits (163), Expect = 2e-12
 Identities = 31/131 (23%), Positives = 57/131 (43%), Gaps = 6/131 (4%)

Query: 230 PSDKDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE 288
           P         L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86

Query: 289 AALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDES-----RILQHQVGSPIT 343
            A+  LN   + GK I++  S+    +     Q +Q L +D       R  +    +   
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 344 NSPPGNWVQFS 354
             PP   +  S
Sbjct: 147 IFPPSATLHLS 157

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score =  115 bits (290), Expect = 1e-29
 Identities = 44/189 (23%), Positives = 72/189 (38%), Gaps = 34/189 (17%)

Query: 152 SRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           +  L V N+N   V    L  LF  YGD++ +      +   ++   D   A+ AM  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 211 NKPLRRRKLDIHFS------IPKDNPSDKDLNQG-------------------------T 239
              L  + + I  S      +P++   D+ L +                          T
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           L + N+ PSVS EDL+ +F + G  VK  +     R    I+   V  A  AL  L+  D
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 299 IA-GKRIKL 306
           +     +++
Sbjct: 183 LGENHHLRV 191

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 71.1 bits (174), Expect = 4e-14
 Identities = 44/215 (20%), Positives = 82/215 (38%), Gaps = 28/215 (13%)

Query: 235 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 293
           +    L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 60

Query: 294 LNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQF 353
           LN   + GK I++  S+    +     Q +Q L +D      H               +F
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH---------------RF 105

Query: 354 SSPIEHNPLQTISKSPN--FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRG-- 409
             P   N       S      N+ P+ S     L  +       ++      KD+     
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEED--LKVLFSSNGGVVKGFKFFQKDRKMALI 163

Query: 410 --SLMEHALTNTISANGASFQQSN----SFSEPKI 438
               +E A+   I  +     +++    SFS+  I
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 55.7 bits (134), Expect = 7e-09
 Identities = 28/101 (27%), Positives = 40/101 (39%), Gaps = 6/101 (5%)

Query: 126 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYT 184
           GN  LH     G+       P    PS TL + NI  +V + +L+ LF   G + +    
Sbjct: 98  GNSPLHRFKKPGSKNFQNIFP----PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 153

Query: 185 ACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RKLDIHFS 224
             K R   +I    +  A  A+  L N  L     L + FS
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  117 bits (294), Expect = 4e-29
 Identities = 35/192 (18%), Positives = 68/192 (35%), Gaps = 11/192 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
               L V N+  ++   +   L   +G +   +        + +G+    Y    +A  A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNED-LRQIFGAYGEV 264
              L  KPL  R L +H++      +   L+   L V  L P  ++ D L +   A    
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAG-QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 265 KEIRETPHKR-HHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 320
              +    +    K    +E+     AE A +  +   + G  +++    PG   R+++ 
Sbjct: 213 TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLA 272

Query: 321 QLNQELEQDESR 332
            L        +R
Sbjct: 273 ALIAAQATALNR 284

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  108 bits (273), Expect = 2e-26
 Identities = 29/169 (17%), Positives = 62/169 (36%), Gaps = 17/169 (10%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
            R + +R +  +V + E+  L   Y  ++  +   K++G   ++  +   A  A+ A   
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 212 KPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--E 269
             LR R+L +                  L V NL PS++ +   ++   +G ++      
Sbjct: 80  SRLRERELSVQLQPTDAL----------LCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 270 TPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 315
           +      K   F E+    +A  A   L    +  + + +  +  G   
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 178

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 64.6 bits (158), Expect = 2e-11
 Identities = 15/104 (14%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 209 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 268
           L  + +R+R         +    ++      +++  L   V+N+++  +   Y  +K   
Sbjct: 3   LDPEEIRKR-----LEHTERQFRNR----RKILIRGLPGDVTNQEVHDLLSDYE-LKYCF 52

Query: 269 ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 312
              +K    F+   +   AEAA+ + ++S +  + + ++     
Sbjct: 53  VDKYKG-TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 53.1 bits (128), Expect = 1e-07
 Identities = 17/90 (18%), Positives = 25/90 (27%), Gaps = 13/90 (14%)

Query: 149 EHPSRTLFVRNINSNVEDSE-LRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 199
              SR L V  +     D + L              T C+         +GF ++ Y   
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSP----TFCQLACGQDGQLKGFAVLEYETA 236

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
             A  A +      L    L + F  P   
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  109 bits (275), Expect = 7e-28
 Identities = 30/169 (17%), Positives = 67/169 (39%), Gaps = 7/169 (4%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAART 204
                 LF+ N+N N   +EL+    +      L         +R F  + +        
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 264
           A+  L    +   ++ +     +D+   +     TL+  NL  +++ ++L+++F    E+
Sbjct: 70  AL-ELTGLKVFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEI 126

Query: 265 KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG 313
           + + +    +   +IEF     AE  L+    ++I G+ + L  +   G
Sbjct: 127 RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 69.6 bits (171), Expect = 7e-14
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDV 284
               +      L + NL+P+ S  +L+          ++         ++   +++F   
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 285 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
              E AL+ L    + G  IKLE  +   +++
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKGRDSKK 95

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  108 bits (272), Expect = 4e-26
 Identities = 37/175 (21%), Positives = 67/175 (38%), Gaps = 16/175 (9%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LYTAC--KHRGFVMISYYDIRAA 202
                 TL++ N   +     +R L +    +     L +      R F  I       A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 203 RTAMRALQNKPLRRRKLDIHFSIP--KDNPSDKDLNQG-TLVVFNLDPSVSNED-LRQIF 258
           R  +  L    +    L    S P  K   +D    +G  +++ NL   + +E+ LR+ F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 259 GAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
             +G +++I       E        F+ F +  +AE AL+ +NRS +  + I + 
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS 286

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  101 bits (254), Expect = 8e-24
 Identities = 31/182 (17%), Positives = 61/182 (33%), Gaps = 20/182 (10%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQ 210
           T+ V+N+  +   +++   F+  G I  +  A    K+  F  I +     A  A+    
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 211 NKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET 270
               +   +  H +            + TL + N  PS +  ++R +      V      
Sbjct: 103 KVVGQNEIIVSHLT------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 271 PHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQE 325
           P  R +      +I+      A   ++ LN   I G  +  + S P    +       + 
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEG 210

Query: 326 LE 327
            E
Sbjct: 211 RE 212

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 63.5 bits (155), Expect = 5e-11
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 4/85 (4%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYD 283
            +    ++    T++V NL  S +   + + F   G +  +      + +     IEF  
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEP 308
              A AA+   ++  +    I +  
Sbjct: 91  YDGALAAITKTHKV-VGQNEIIVSH 114

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  101 bits (255), Expect = 4e-25
 Identities = 35/171 (20%), Positives = 69/171 (40%), Gaps = 16/171 (9%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIRAART 204
           +  +FV  +     + +LR LFEQYG +  +           + +G   +++Y  +AA  
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 264
           A  AL N  +           P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 265 KEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           +E R         R   F+ F     A+ A+K+++       +     S P
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH-----QAQTMEGCSSP 168

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 63.0 bits (154), Expect = 1e-11
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHK---FIEFYDVRAAE 288
           +   + V  +  + S +DLR++F  YG V EI      + +    K   F+ FY  +AA 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 289 AALKSLNRSDIAGKRIKLEPSRPGGARRN 317
            A  +L+   +          +P  + +N
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKN 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 99.6 bits (249), Expect = 2e-24
 Identities = 36/166 (21%), Positives = 68/166 (40%), Gaps = 16/166 (9%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAARTA 205
           +  L V  +  ++ D EL ALF   G       +R   T     G+  + +     ++ A
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTG-YSYGYAFVDFTSEMDSQRA 61

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 265
           ++ L    +R ++L + ++     P  + +    L V NL  +++++ L  IFG YG + 
Sbjct: 62  IKVLNGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIV 117

Query: 266 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
           +        T   R   F+ +     A+ A+ +LN     G    L
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 163

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 67.2 bits (165), Expect = 4e-13
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAA 290
           +   L+V  L   +++ +L  +F A G +   R        +     F++F     ++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 291 LKSLNRSDIAGKRIKLEPSRPGGARRN 317
           +K LN   +  KR+K+  +RPGG    
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIK 88

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 41.4 bits (98), Expect = 3e-04
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
               L+V N+   + D +L  +F +YG I            + RG   + Y     A+ A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 206 MRALQNKPL 214
           + AL N   
Sbjct: 148 ISALNNVIP 156

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 99.6 bits (249), Expect = 2e-24
 Identities = 26/169 (15%), Positives = 60/169 (35%), Gaps = 20/169 (11%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIRA 201
           +R L+V NI   + +  +   F     +  L  A           + + F  + +  +  
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 202 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY 261
              AM A      + + L I                  L +  L   ++++ ++++  ++
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLP----GAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 262 GEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
           G +K         T   + + F E+ D+   + A+  LN   +  K++ 
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 46.8 bits (112), Expect = 4e-06
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 145 HPYGEHPS-RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYD 198
           H Y   P    LF+  + + + D +++ L   +G ++             +G+    Y D
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 199 IRAARTAMRALQNKPLRRRKLDI 221
           I     A+  L    L  +KL +
Sbjct: 146 INVTDQAIAGLNGMQLGDKKLLV 168

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 97.0 bits (242), Expect = 4e-23
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 32/194 (16%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIR 200
            +R L+V NI   + +  +   F     +  L  A           + + F  + +  + 
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG----------------TLVVFN 244
               AM A      + + L I              N                   L +  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 245 LDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           L   ++++ ++++  ++G +K         T   + + F E+ D+   + A+  LN   +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

Query: 300 AGKRIKLEPSRPGG 313
             K++ ++ +  G 
Sbjct: 182 GDKKLLVQRASVGA 195

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.4 bits (243), Expect = 4e-23
 Identities = 33/176 (18%), Positives = 81/176 (46%), Gaps = 17/176 (9%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 202
                  ++V +I   + +  +R  F  +G I+++  +      KH+GF  + Y    AA
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPK-------DNPSDKDLNQGTLVVFNLDPSVSNEDLR 255
           + A+  + +  L  R + +             D  +++      + V ++   +S++D++
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143

Query: 256 QIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
            +F A+G++K         T   + + FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 67.7 bits (166), Expect = 6e-13
 Identities = 25/130 (19%), Positives = 48/130 (36%), Gaps = 12/130 (9%)

Query: 204 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 263
           + M ++       R                      + V ++   +  + +RQ F  +G 
Sbjct: 2   SHMASMTGGQQMGRG-------SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP 54

Query: 264 VKEIR--ETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
           +K I          HK   F+E+    AA+ AL+ +N   + G+ IK+      G  + +
Sbjct: 55  IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 114

Query: 319 MLQLNQELEQ 328
           + QL +E   
Sbjct: 115 IDQLAEEARA 124

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 52.7 bits (127), Expect = 8e-08
 Identities = 16/86 (18%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
               ++V +++ ++ D +++++FE +G I++   A      KH+G+  I Y   ++++ A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPS 231
           + ++    L  + L +  ++    P 
Sbjct: 184 VSSMNLFDLGGQYLRVGKAVTPPMPL 209

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 96.6 bits (241), Expect = 7e-23
 Identities = 36/204 (17%), Positives = 85/204 (41%), Gaps = 10/204 (4%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 203
            +P  +L+V +++ +V ++ L   F   G I ++         +  G+  +++     A 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 204 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 263
            A+  +    ++ + + I +S     PS +    G + + NLD S+ N+ L   F A+G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRD--PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129

Query: 264 VKEIR---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 320
           +   +   +    + + F+ F    AAE A++ +N   +  +++ +   +    R   + 
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

Query: 321 QLNQELEQDESRILQHQVGSPITN 344
              +E    +        G  +T+
Sbjct: 190 ARAKEFYPYDVPDYAGSSGRIVTD 213

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 65.8 bits (161), Expect = 3e-12
 Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYD 283
           NPS       +L V +L P V+   L + F   G +  IR      T     + ++ F  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
              AE AL ++N   I GK +++  S+   + R
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQRDPSLR 99

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 94.6 bits (236), Expect = 1e-22
 Identities = 39/167 (23%), Positives = 67/167 (40%), Gaps = 16/167 (9%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAARTA 205
              L V  +  N+   E R+LF   G+I +     +        G+  ++Y D + A  A
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESC-KLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 265
           +  L    L+ + + + ++ P    S   +    L V  L  +++ ++L Q+F  YG + 
Sbjct: 61  INTLNGLRLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116

Query: 266 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
             R      T   R   FI F     AE A+K LN    +G    + 
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 67.6 bits (166), Expect = 2e-13
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAA 290
           ++  L+V  L  +++ E+ R +FG+ GE++  +    K         F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 291 LKSLNRSDIAGKRIKLEPSRPGGAR 315
           + +LN   +  K IK+  +RP  A 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSAS 85

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 88.8 bits (221), Expect = 2e-21
 Identities = 19/85 (22%), Positives = 44/85 (51%), Gaps = 6/85 (7%)

Query: 149 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAA 202
             P+ T+++ N+N  ++  EL+    A+F ++G I    +  + K RG   + + ++ +A
Sbjct: 5   TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPK 227
             A+R++Q  P   + + I ++   
Sbjct: 65  TNALRSMQGFPFYDKPMRIQYAKTD 89

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 61.5 bits (150), Expect = 7e-12
 Identities = 19/94 (20%), Positives = 47/94 (50%), Gaps = 12/94 (12%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHK 277
           ++P+  P+       T+ + NL+  +  ++L++    IF  +G++ +I    +   R   
Sbjct: 1   AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQA 54

Query: 278 FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           F+ F +V +A  AL+S+       K ++++ ++ 
Sbjct: 55  FVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 93.6 bits (233), Expect = 2e-21
 Identities = 48/196 (24%), Positives = 75/196 (38%), Gaps = 19/196 (9%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 213
            LFV N+ +++ + + + LFE+YG+   ++   + RGF  I       A  A   L    
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTI 82

Query: 214 LRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----E 269
           L+ R L I F+               L V NL P VSNE L Q F  +G V++      +
Sbjct: 83  LKSRPLRIRFATHGAA----------LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD 132

Query: 270 TPHKRHHKFIEFYDVRAAEAALKSLNRSDI----AGKRIKLEPSRPGGARRNLMLQLNQE 325
                   F+EF     A  AL+             + + +EP         L  +L Q+
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQK 192

Query: 326 LEQDESRILQHQVGSP 341
            +Q      Q    + 
Sbjct: 193 TQQYHKEREQPPRFAQ 208

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 68.2 bits (167), Expect = 9e-13
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 226 PKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV 284
               P +K   Q   L V NL   ++ ED +++F  YGE  E+      R   FI     
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVF-INRDRGFGFIRLESR 68

Query: 285 RAAEAALKSLNRSDIAGKRIKLEPSRPG 312
             AE A   L+ + +  + +++  +  G
Sbjct: 69  TLAEIAKAELDGTILKSRPLRIRFATHG 96

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 47.4 bits (113), Expect = 6e-06
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 4/67 (5%)

Query: 150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTA 205
                L V+N++  V +  L   F Q+G +           +  G   + +     AR A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

Query: 206 MRALQNK 212
           +    + 
Sbjct: 154 LERCGDG 160

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 90.7 bits (226), Expect = 3e-21
 Identities = 34/167 (20%), Positives = 70/167 (41%), Gaps = 19/167 (11%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAART 204
           R L+V N++  + +  L+  F+  G I        +      K+  +  + Y+    A  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN----NKNVNYAFVEYHQSHDANI 56

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 264
           A++ L  K +    + I+++      S  D +   L V +L+ +V +E LR  F  +   
Sbjct: 57  ALQTLNGKQIENNIVKINWAFQ-SQQSSSD-DTFNLFVGDLNVNVDDETLRNAFKDFPSY 114

Query: 265 KEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 306
                    +T   R + F+ F     A+ A+ S+   D+ G+ +++
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 64.5 bits (158), Expect = 3e-12
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 294
            L V NLD +++ + L+Q F   G +  I+    +     ++ F+E++    A  AL++L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 295 NRSDIAGKRIKLEPSRPGGARRN 317
           N   I    +K+  +       +
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSS 84

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 13/78 (16%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRA 201
            +  LFV ++N NV+D  LR  F+ +    +                RG+  +S+     
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLS----GHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 202 ARTAMRALQNKPLRRRKL 219
           A+ AM ++Q + L  R L
Sbjct: 142 AQNAMDSMQGQDLNGRPL 159

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 87.6 bits (218), Expect = 3e-20
 Identities = 31/174 (17%), Positives = 68/174 (39%), Gaps = 25/174 (14%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAA 202
           S  +F+  +N +  +  LR  F +YG +    T           + RGF  +S+    + 
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTV----TDLKIMKDPATGRSRGFGFLSFEKPSSV 58

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG 262
              ++      L  + +D   +IP+D         G + V  + P V  ++  + F  +G
Sbjct: 59  DEVVKTQHI--LDGKVIDPKRAIPRDEQD----KTGKIFVGGIGPDVRPKEFEEFFSQWG 112

Query: 263 EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
            + +      ++T   R   F+ +    A +   +     D   ++I+++ + P
Sbjct: 113 TIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP 165

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 48.3 bits (116), Expect = 1e-06
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 14/87 (16%)

Query: 150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIR 200
             +  +FV  I  +V   E    F Q+G I                + RGF  ++Y    
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTI----IDAQLMLDKDTGQSRGFGFVTYDSAD 140

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPK 227
           A        +    + RK++I  + P+
Sbjct: 141 AVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 87.4 bits (217), Expect = 7e-20
 Identities = 39/196 (19%), Positives = 73/196 (37%), Gaps = 29/196 (14%)

Query: 144 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 194
           E P      R LF+  ++    D  LR+ FEQ+G +    T C         + RGF  +
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60

Query: 195 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVF--NLDPSVSNE 252
           +Y  +     AM A +   +  R ++   ++ +++      +     +F   +       
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 253 DLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI--- 304
            LR  F  YG+++ I     R +  KR   F+ F D  + +  +       + G      
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 305 ----KLEPSRPGGARR 316
               K E +    ++R
Sbjct: 179 KALSKQEMASASSSQR 194

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 51.5 bits (124), Expect = 1e-07
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYY 197
            + P      + +FV  I  + E+  LR  FEQYG I  +         K RGF  +++ 
Sbjct: 95  SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 198 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
           D  +    +   +   +     ++  ++ K   +
Sbjct: 155 DHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMA 187

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 49.2 bits (118), Expect = 1e-06
 Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 8/98 (8%)

Query: 225 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFI 279
           + K     +      L +  L    ++E LR  F  +G + +        T   R   F+
Sbjct: 1   MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 280 EFYDVRAAEAALKSLNRSDIAGKRI--KLEPSRPGGAR 315
            +  V   +AA+ +     + G+ +  K   SR    R
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 84.5 bits (209), Expect = 7e-20
 Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 3/103 (2%)

Query: 138 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY 197
            G+    H     PSR + +R +  +V + E+ +L   +G + T     K +    I   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV-TNLLMLKGKNQAFIEMN 60

Query: 198 DIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLNQG 238
              AA T +    +    LR + + I FS  K+  +D   NQ 
Sbjct: 61  TEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 103

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNR 296
            + +  L   V+  ++  +   +G+V  +     K +  FIE     AA   +   +   
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 76

Query: 297 SDIAGKRIKLEPSRP 311
             + G+ I ++ S  
Sbjct: 77  PVLRGQPIYIQFSNH 91

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 83.0 bits (205), Expect = 4e-19
 Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 6/98 (6%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISY 196
           G  P    PS+ + + NIN  V   +L+    AL    GDI    +  +  + G   I +
Sbjct: 20  GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVF 79

Query: 197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD 234
               +A+  + A Q  P +   L I FS    +   +D
Sbjct: 80  ATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 71.1 bits (174), Expect = 6e-15
 Identities = 15/92 (16%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHKFI 279
               P   + +Q  +++ N++P V  E L+     +  + G++ +I    +       +I
Sbjct: 19  LGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77

Query: 280 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
            F    +A+A +++       G  + +  S  
Sbjct: 78  VFATQESAQAFVEAFQGYPFQGNPLVITFSET 109

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 82.7 bits (204), Expect = 5e-19
 Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 6/113 (5%)

Query: 131 HYSVPNGA---GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 187
           H+   +G    G+  G+      PSR + +R +  +V + E+ +L   +G +       K
Sbjct: 7   HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN-LLMLK 65

Query: 188 HRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLNQG 238
            +    I      AA T +    +    LR + + I FS  K+  +D   NQ 
Sbjct: 66  GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 118

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.2 bits (130), Expect = 4e-09
 Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 9/112 (8%)

Query: 202 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY 261
             +      +  L  R   +  S     PS        + +  L   V+  ++  +   +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR------VIHIRKLPIDVTEGEVISLGLPF 55

Query: 262 GEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNRSDIAGKRIKLEPSRP 311
           G+V  +     K +  FIE     AA   +   +     + G+ I ++ S  
Sbjct: 56  GKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 77.4 bits (191), Expect = 3e-17
 Identities = 20/89 (22%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNR 296
            L + NL   ++ E++  IFG YG +++IR   TP  R   ++ + D+  A+ A+  L+ 
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 297 SDIAGKRIKLEPSRPGGARRNLMLQLNQE 325
            +++ + + +       A + +  +  +E
Sbjct: 70  FNVSNRYLVVLYYNANRAFQKMDTKKKEE 98

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 74.3 bits (183), Expect = 3e-16
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMR 207
            +R L++RN+   +   E+  +F +YG    IR   T  + RG   + Y DI  A+ A+ 
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP-ETRGTAYVVYEDIFDAKNAVD 65

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPSDKDL 235
            L    +  R L + +          D 
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDT 93

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 76.5 bits (189), Expect = 3e-17
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 285
           P  +   +     TL+  NL  +++ ++L+++F    E++ + +    +   +IEF    
Sbjct: 7   PCTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 286 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
            AE  L+    ++I G+ + L  +   G  R
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 18/83 (21%), Positives = 37/83 (44%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 208
              +RTL  +N++ N+ + EL+ +FE   +IR +    K +G   I +     A   +  
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 209 LQNKPLRRRKLDIHFSIPKDNPS 231
            Q   +  R + ++++  K    
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 95

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RS 297
            L + NL P+V+ +DLRQ+FG         +   K  + F+++ D   A  A+++L+ + 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 298 DIAGKRIKLEPSRPGGARR 316
           ++ GK ++++ S     R 
Sbjct: 69  ELHGKIMEVDYSVSKKLRS 87

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 59.2 bits (144), Expect = 4e-11
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 2/88 (2%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 205
             G      L++ N++  V   +LR LF                G+  + Y D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRA 60

Query: 206 MRALQNKP-LRRRKLDIHFSIPKDNPSD 232
           +  L  K  L  + +++ +S+ K   S 
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRSS 88

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 73.1 bits (180), Expect = 5e-16
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 1/81 (1%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 285
                        T  + N+    +  DL  +F  +G + + +    ++   FI++    
Sbjct: 16  VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKGCCFIKYDTHE 74

Query: 286 AAEAALKSLNRSDIAGKRIKL 306
            A   + +L      G+ ++ 
Sbjct: 75  QAAVCIVALANFPFQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
             T ++ NI     +++L  LF+ +G I         +G   I Y     A   + AL N
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-YPEKGCCFIKYDTHEQAAVCIVALAN 85

Query: 212 KPLRRRKL 219
            P + R L
Sbjct: 86  FPFQGRNL 93

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 74.9 bits (184), Expect = 6e-16
 Identities = 31/154 (20%), Positives = 53/154 (34%), Gaps = 17/154 (11%)

Query: 175 QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN----------KPLRRRKLDIHFS 224
           QY  I    T     G       D   A    +   N              +       S
Sbjct: 2   QYKLILNGKTLK---GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGS 58

Query: 225 IPKDNPSDKD--LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY 282
               +   +D       + V NL  + +  +L + FG YG ++ +    +     F+EF 
Sbjct: 59  HHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFE 118

Query: 283 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
           D R A  A++ L+   + G R+++E S     +R
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELSNGE--KR 150

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 64.9 bits (158), Expect = 2e-12
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 144 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 203
            H         ++V N+ +N   +EL   F  YG +R+++ A    GF  + + D R A 
Sbjct: 65  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAA 124

Query: 204 TAMRALQNKPLRRRKLDIHFSIPK 227
            A+R L  + L   ++ +  S  +
Sbjct: 125 DAVRELDGRTLCGCRVRVELSNGE 148

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.5 bits (181), Expect = 6e-16
 Identities = 21/107 (19%), Positives = 44/107 (41%), Gaps = 4/107 (3%)

Query: 210 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE 269
            +       L    S    +  + +L+   L V      V   +L +IFG +G +KE++ 
Sbjct: 5   HHHHHHSSGLVPRGS-HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

Query: 270 TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
                   F+EF +  +A  A++ ++    A + +++  S+    R 
Sbjct: 64  ---LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 61.9 bits (151), Expect = 7e-12
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           GE  +  LFVR    +V++SEL  +F  +G ++         GF  + + +  +A  A+ 
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMK---EVKILNGFAFVEFEEAESAAKAIE 83

Query: 208 ALQNKPLRRRKLDIHFSIPKDN 229
            +  K    + L++ +S     
Sbjct: 84  EVHGKSFANQPLEVVYSKLPAK 105

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 21/74 (28%), Positives = 34/74 (45%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 303
           NL       +L + F  YG ++ +    +     F+EF D R AE A++ L+   I G R
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

Query: 304 IKLEPSRPGGARRN 317
           +++E S     R  
Sbjct: 67  VRVELSTGMPRRSR 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 59.2 bits (144), Expect = 5e-11
 Identities = 22/80 (27%), Positives = 36/80 (45%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           ++V N+ +     EL   F  YG +RT++ A    GF  + + D R A  A+R L  K +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 215 RRRKLDIHFSIPKDNPSDKD 234
              ++ +  S      S  D
Sbjct: 63  CGSRVRVELSTGMPRRSRFD 82

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 71.8 bits (177), Expect = 1e-15
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALK 292
            + +  L  +V+ + + +IF  YG++K I            + + ++EF +   AE ALK
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 293 SLNRSDIAGKRIKLEPSRP 311
            ++   I G+ I       
Sbjct: 66  HMDGGQIDGQEITATAVLA 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 49.8 bits (120), Expect = 6e-08
 Identities = 9/85 (10%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRGFVMISYYDIRAART 204
               + +  +  NV    +  +F  YG I+ +            +G+  + + +   A  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDN 229
           A++ +    +  +++     +    
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 72.4 bits (178), Expect = 1e-15
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALK 292
           N   + V NL P +  +D+  +F  YG +++I +  ++R      F+EF D R AE A+ 
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI-DLKNRRGGPPFAFVEFEDPRDAEDAVY 79

Query: 293 SLNRSDIAGKRIKLEPSRPGGARR 316
             +  D  G R+++E  R G    
Sbjct: 80  GRDGYDYDGYRLRVEFPRSGRGTG 103

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 56.6 bits (137), Expect = 5e-10
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 2/94 (2%)

Query: 133 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH--RG 190
           S  +G            +    ++V N+  ++   ++  +F +YG IR +    +     
Sbjct: 3   SGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP 62

Query: 191 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 224
           F  + + D R A  A+           +L + F 
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 96

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 1/95 (1%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RETPHKRHHKFIEFY 282
           S      S       TLV+ NL  S + E L+++F     +K    +    + + FIEF 
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFA 61

Query: 283 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
               A+ AL S N+ +I G+ I+LE   P G+  +
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNS 96

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 61.1 bits (149), Expect = 1e-11
 Identities = 18/97 (18%), Positives = 44/97 (45%), Gaps = 4/97 (4%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIR--TLYTACKHRGFVMI 194
           G+   +G   +    S+TL + N++ +  +  L+ +FE+   I+        K +G+  I
Sbjct: 1   GSSGSSGNSTWSG-ESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNG-KSKGYAFI 58

Query: 195 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
            +     A+ A+ +   + +  R + +    P+ +P+
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 71.5 bits (176), Expect = 2e-15
 Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           TL V NL    S + LR++F  YG V ++       T   R   F+ F+D R A+ A  +
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 294 LNRSDIAGKRIKLEPSRPGGARRN 317
           ++ +++ G+ ++++ +R G    +
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLS 98

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 57.6 bits (140), Expect = 2e-10
 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 142 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 196
           +G          TL V N+        LR +FE+YG +  +Y          RGF  + +
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62

Query: 197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPK 227
           +D R A+ A  A+    L  R+L +  +   
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.7 bits (176), Expect = 2e-15
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK---FIEFYDVRAAEAALKS 293
            +    L+ +V    L+ +   YGEV+E+     P  R H     + F   R A+  +K+
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 294 LNRSDIAGKRIKLEPSRPGGARR 316
           L+ + + G  I  +    G  R 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRM 90

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 202
           G+ P + +    +N NV ++ L+ +  +YG++  +         KH G   + +   R A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDN 229
           +  ++ L    +    +     I    
Sbjct: 62  KETVKNLHLTSVMGNIIHAQLDIKGQQ 88

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 71.2 bits (175), Expect = 3e-15
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L V NL  S S E + + F        +      R + F+ F +   A  A+K+LN   
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGA-VERVKKIRDYAFVHFSNREDAVEAMKALNGKV 75

Query: 299 IAGKRIKLEPSRP 311
           + G  I++  ++P
Sbjct: 76  LDGSPIEVTLAKP 88

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
             + L+VRN+  +  +  +   F             K R +  + + +   A  AM+AL 
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALN 72

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
            K L    +++  + P D  S
Sbjct: 73  GKVLDGSPIEVTLAKPVDKDS 93

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.1 bits (175), Expect = 3e-15
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVR 285
              + D    TL V NL   V+   + Q+F   G  K  +       +    F+EFY+ R
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 286 AAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
            A AAL ++N   I GK +K+  +    ++++
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 17/96 (17%), Positives = 45/96 (46%), Gaps = 4/96 (4%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYTACKHRGFVM 193
           G+   +G     +   RTL+V N++ +V +  +  LF Q G     + +     +  +  
Sbjct: 1   GSSGSSGMME-DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF 59

Query: 194 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
           + +Y+ R A  A+ A+  + +  +++ ++++    +
Sbjct: 60  VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 95

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 70.7 bits (174), Expect = 4e-15
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA 289
                  +  L V NL P ++ E++R++F  YG+  E+      +   FI       AE 
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEI 66

Query: 290 ALKSLNRSDIAGKRIKLEPSRPGGARR 316
           A   L+   + GK++++  +    +  
Sbjct: 67  AKVELDNMPLRGKQLRVRFACHSASLT 93

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 60.7 bits (148), Expect = 1e-11
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
               LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L 
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELD 72

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
           N PLR ++L + F+    + +
Sbjct: 73  NMPLRGKQLRVRFACHSASLT 93

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 71.2 bits (175), Expect = 4e-15
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 228 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 287
           D  +       T+    +   ++++ +RQ F  +G++ EIR  P K  + F+ F    +A
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YSFVRFSTHESA 74

Query: 288 EAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
             A+ S+N + I G  +K    +      +
Sbjct: 75  AHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.3 bits (131), Expect = 3e-09
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           + T++   I S + D  +R  F  +G I  +      +G+  + +    +A  A+ ++  
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEI-RVFPEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 212 KPLRRRKLDIHFSIPKDNPSD 232
             +    +  ++     + + 
Sbjct: 84  TTIEGHVVKCYWGKESPDMTS 104

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 72.6 bits (178), Expect = 5e-15
 Identities = 28/143 (19%), Positives = 56/143 (39%), Gaps = 14/143 (9%)

Query: 189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG---------T 239
           +G       D   A    +   N      +     +      ++   +           +
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           L V NL    S + LR++F  YG V ++     R T   R   F+ F+D R AE A+ ++
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

Query: 295 NRSDIAGKRIKLEPSRPGGARRN 317
           + + + G+ ++++ +R G    +
Sbjct: 133 DGAVLDGRELRVQMARYGRPPDS 155

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 56.0 bits (135), Expect = 3e-09
 Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 135 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHR 189
               G+    H        +L V N+        LR +FE+YG +  +Y        + R
Sbjct: 53  TVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 112

Query: 190 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 230
           GF  + ++D R A  AM A+    L  R+L +  +     P
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 70.4 bits (173), Expect = 5e-15
 Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L V NL  +V+ E L + F  +G+++ +++    + + FI F +   A  A++ +N  D
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKK---LKDYAFIHFDERDGAVKAMEEMNGKD 69

Query: 299 IAGKRIKLEPSRPGGARRN 317
           + G+ I++  ++P   +R 
Sbjct: 70  LEGENIEIVFAKPPDQKRK 88

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 60.8 bits (148), Expect = 1e-11
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRAL 209
             + LFVRN+ + V +  L   F Q+G +       K  + +  I + +   A  AM  +
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKL----ERVKKLKDYAFIHFDERDGAVKAMEEM 65

Query: 210 QNKPLRRRKLDIHFSIPKDNPSDKDLNQ 237
             K L    ++I F+ P D    +   Q
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQ 93

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 72.1 bits (177), Expect = 6e-15
 Identities = 25/118 (21%), Positives = 48/118 (40%), Gaps = 6/118 (5%)

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 264
           A+R+     L + + D HF    +          TL V NL    + E + ++F   G++
Sbjct: 8   ALRSDSYVELSQYR-DQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 265 KEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           K+I     +         F+E+Y    AE A++ +N + +  + I+ +        R 
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 56.7 bits (137), Expect = 1e-09
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
            S TL+V N++    + ++  LF + GDI+ +            GF  + YY    A  A
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           MR +    L  R +   +      
Sbjct: 98  MRYINGTRLDDRIIRTDWDAGFKE 121

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 69.7 bits (171), Expect = 1e-14
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 4/91 (4%)

Query: 228 DNPSDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA 286
            N +D       + + NL+ + V   D+  IF  YG V         + + F+++ + R 
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS---VHKGYAFVQYSNERH 74

Query: 287 AEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           A AA+   N   +AG+ + +  +      R+
Sbjct: 75  ARAAVLGENGRVLAGQTLDINMAGEPKPDRS 105

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 56.2 bits (136), Expect = 7e-10
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 151 PSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRA 208
            +  +F+ N+N+  V+ S++  +F +YG +      C  H+G+  + Y + R AR A+  
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVA----GCSVHKGYAFVQYSNERHARAAVLG 81

Query: 209 LQNKPLRRRKLDIHFSIPKDNP 230
              + L  + LDI+ +      
Sbjct: 82  ENGRVLAGQTLDINMAGEPKPD 103

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE- 288
            S +D    TL V  L  +++  DLR  F  +GE++ I     ++   FI+F   +AAE 
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEV 63

Query: 289 AALKSLNRSDIAGKRIKL 306
           AA KS N+  + G+R+ +
Sbjct: 64  AAEKSFNKLIVNGRRLNV 81

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 196
           G+   +GE         TL+V  +   + +++LR  F Q+G+IRT+ T  + +    I +
Sbjct: 1   GSSGSSGEDK----TITTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQF 55

Query: 197 YDIRAARTAMRALQNK 212
              +AA  A     NK
Sbjct: 56  ATRQAAEVAAEKSFNK 71

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L V  L P+ S   L + F  +G ++ I          +I++  + AA+AA   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 299 IAG--KRIKLEPSRPGGAR 315
           + G  +R++++ ++ G + 
Sbjct: 78  LGGPDRRLRVDFAKSGPSS 96

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           P+  L+V  +  N   + L   F+++G IRT+    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMR 74

Query: 211 NKPLRRRKLDIHFSIPKDNPSD 232
             PL      +     K  PS 
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPSS 96

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 67.6 bits (166), Expect = 4e-14
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 301
           V N+  + ++++LR +F   G V E       + + F+       A+AA+  LN  ++ G
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAAIAQLNGKEVKG 70

Query: 302 KRIKLEPSRPGGARR 316
           KRI +E S  G  + 
Sbjct: 71  KRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.8 bits (143), Expect = 5e-11
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
            +  +FV N+++     ELR+LFE+ G +         + +  +       A+ A+  L 
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVI---ECDVVKDYAFVHMEKEADAKAAIAQLN 64

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
            K ++ +++++  S      S
Sbjct: 65  GKEVKGKRINVELSTKGQKKS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 67.2 bits (165), Expect = 5e-14
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 303
           NL    + +++R +F  YG+V E       +++ F+   D  AAE A+++L+   + G  
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 304 IKLEPSRPGGARRN 317
           I +E S+      +
Sbjct: 72  INVEASKNKSKASS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           G      LF+ N+     + E+R+LFEQYG +         + +  +   D  AA  A+R
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVL---ECDIIKNYGFVHIEDKTAAEDAIR 60

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPS 231
            L +  L    +++  S  K   S
Sbjct: 61  NLHHYKLHGVNINVEASKNKSKAS 84

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 67.2 bits (165), Expect = 5e-14
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 294 LNRSDIAGKRIKLEPSRPG 312
            N  ++ G+RI++     G
Sbjct: 77  ANGMELDGRRIRVSGPSSG 95

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGF 191
           G+   +G     + P+  L V  ++    + +LR +F +YG I  +         + RGF
Sbjct: 1   GSSGSSGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59

Query: 192 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 224
             + + ++  A+ A        L  R++ +   
Sbjct: 60  AFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 66.9 bits (164), Expect = 8e-14
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 301
           V N+ P+ +N++LR  F  YG V E       + + F+       A  A++ L+ ++  G
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECDI---VKDYAFVHMERAEDAVEAIRGLDNTEFQG 71

Query: 302 KRIKLEPSRPGGARRN 317
           KR+ ++ S       +
Sbjct: 72  KRMHVQLSTSRLRTAS 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 58.0 bits (141), Expect = 9e-11
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
            S  L V NI+    + ELRA FE+YG +         + +  +       A  A+R L 
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPVI---ECDIVKDYAFVHMERAEDAVEAIRGLD 65

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
           N   + +++ +  S  +   +
Sbjct: 66  NTEFQGKRMHVQLSTSRLRTA 86

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 67.3 bits (165), Expect = 9e-14
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 6/96 (6%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 280
           P DN S ++ +  T+    L   +   DL   F A G+V+++     R +   +   ++E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
           F ++++   A+  L    + G  I ++ S+    R 
Sbjct: 74  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRL 108

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 48.1 bits (115), Expect = 5e-07
 Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 6/102 (5%)

Query: 133 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 187
           S  +            E  +RT+F   + + +   +L   F   G +R +         +
Sbjct: 6   SGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR 65

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
            +G   + + +I++   A+  L  + L    + +  S  + N
Sbjct: 66  SKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN 106

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.5 bits (163), Expect = 1e-13
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 242 VFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 300
           + NL   +VS EDL +IF  YG + +I     K    FI+F + ++   A++  ++    
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 301 GKRIKLEPSRPGGARR 316
           GK++ LE S      +
Sbjct: 72  GKKLILEVSSSNARPQ 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.8 bits (143), Expect = 6e-11
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 151 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRA 208
           P   LF+ N+   NV   +L  +F  YG I            F  I + + ++ R A+  
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM----QINIKNAFGFIQFDNPQSVRDAIEC 64

Query: 209 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 239
              +    +KL +  S     P     + GT
Sbjct: 65  ESQEMNFGKKLILEVSSSNARPQFDHGDHGT 95

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 67.8 bits (166), Expect = 1e-13
 Identities = 27/129 (20%), Positives = 54/129 (41%), Gaps = 6/129 (4%)

Query: 195 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNED 253
           S++    +   +    +         +            D+   T L V NL    S + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63

Query: 254 LRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           LR++F  YG V ++     R T   R   F+ F+D R AE A+ +++ + + G+ ++++ 
Sbjct: 64  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

Query: 309 SRPGGARRN 317
           +R G    +
Sbjct: 124 ARYGRPPDS 132

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 55.9 bits (135), Expect = 1e-09
 Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 5/110 (4%)

Query: 123 SASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL 182
            +    +             G  P       +L V N+        LR +FE+YG +  +
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 183 YTAC-----KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 227
           Y        + RGF  + ++D R A  AM A+    L  R+L +  +   
Sbjct: 78  YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 66.8 bits (163), Expect = 1e-13
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 196
           G+   +G+   G  PSR L +R +   V ++E+ AL   +G +  +    K +    +  
Sbjct: 1   GSSGSSGDKMDGA-PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLEL 58

Query: 197 YDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLN 236
               AA T +         LR + + I +S  K+  +    +
Sbjct: 59  ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGPSS 100

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 227 KDNPSDKDLNQGTLVVF--NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV 284
             +  DK     + V+    L   V+  ++  +   +G+V  I     K +  F+E    
Sbjct: 3   SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATE 61

Query: 285 RAAEAALK--SLNRSDIAGKRIKLEPSR 310
            AA   +   S     +  + I ++ S 
Sbjct: 62  EAAITMVNYYSAVTPHLRNQPIYIQYSN 89

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 66.5 bits (163), Expect = 2e-13
 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L + NL P V+  DL  +F  + E K         T   R   FI F +   A  AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 294 LNRSDIAGKRIKLEPSRPGGAR 315
           +N   + GK + +E  +    R
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQR 108

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 65.0 bits (159), Expect = 7e-13
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYG------DIRTLYTACKHRGFVMISYYDIRAART 204
           P++ L+++N++  V + +L +LF ++           + T  + RG   I++ +   A  
Sbjct: 24  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTG-RMRGQAFITFPNKEIAWQ 82

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSD 232
           A+  +    L  + L I F   K   S 
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 67.5 bits (165), Expect = 2e-13
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIR 200
           P+  ++V+N+  +V++ +L+ +F +Y D  +               + +G   I   + +
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 233
           AA  A++      L  + + + F+       D 
Sbjct: 104 AAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 59.8 bits (145), Expect = 7e-11
 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 227 KDNPSDKDLNQG----TLVVFNLDPSVSNEDLRQIFGAYGEVKE----------IRETPH 272
           +     +    G     + V NL   V  +DL+ IFG Y +             + +   
Sbjct: 31  ETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR 90

Query: 273 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
            +   FI   + +AA  ALK  N   + GK + ++ +R 
Sbjct: 91  MKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 66.2 bits (162), Expect = 2e-13
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V ++      +++++ F  YGE+K I     R T   + +  +E+   + A AA ++
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 294 LNRSDIAGKRIKLEPSRPGGARR 316
           LN ++I G+ I+++     G +R
Sbjct: 88  LNGAEIMGQTIQVDWCFVKGPKR 110

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 56.5 bits (137), Expect = 6e-10
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 5/103 (4%)

Query: 133 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 187
            V N         P        LFV +I+   ++ E++  F  YG+I+ ++         
Sbjct: 7   RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 66

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 230
            +G+ ++ Y   + A  A  AL    +  + + + +   K   
Sbjct: 67  SKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 65.9 bits (161), Expect = 2e-13
 Identities = 10/79 (12%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
            S  + +R +   V +++L    +++G I  +      +   ++ + D+  A  A+    
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYV-VVMPKKRQALVEFEDVLGACNAVNYAA 78

Query: 211 NKP--LRRRKLDIHFSIPK 227
           +    +      +++S  +
Sbjct: 79  DNQIYIAGHPAFVNYSTSQ 97

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.0 bits (143), Expect = 5e-11
 Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 9/100 (9%)

Query: 213 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 272
                 ++ +    K   S        + +  L   V   DL +    +G +  +   P 
Sbjct: 3   HHHHHHMENYDDPHKTPASP------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

Query: 273 KRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSR 310
           KR    +EF DV  A  A+     +   IAG    +  S 
Sbjct: 57  KR-QALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 66.3 bits (162), Expect = 3e-13
 Identities = 26/125 (20%), Positives = 57/125 (45%), Gaps = 10/125 (8%)

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 260
           A    M+   +K +           P      K++++ ++ V N+D   + +DL   F +
Sbjct: 1   AIAPCMQTTHSK-MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 261 YGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR---PG 312
            G +  I     + + H + + +IEF +  + +AA+ +++ +   G+ IK+ P R   PG
Sbjct: 60  CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG 118

Query: 313 GARRN 317
            +  +
Sbjct: 119 ISSTD 123

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 45.5 bits (108), Expect = 5e-06
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 133 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 187
           +   G           E   R+++V N++      +L A F   G I  +   C      
Sbjct: 17  AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH 76

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKL 219
            +G+  I + +  +   A+ A+     R R +
Sbjct: 77  PKGYAYIEFAERNSVDAAV-AMDETVFRGRTI 107

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 66.3 bits (162), Expect = 3e-13
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 294 LNRSDIAGKRIKLEPSRP 311
            N  ++ G+RI+++ S  
Sbjct: 108 ANGMELDGRRIRVDFSIT 125

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 55.5 bits (134), Expect = 2e-09
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
           P+  L V  ++    + +LR +F +YG I  +         + RGF  + + ++  A+ A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 206 MRALQNKPLRRRKLDIHFSIPK 227
                   L  R++ + FSI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 65.4 bits (160), Expect = 4e-13
 Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 15/96 (15%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH----HK-- 277
            +PK   + K      ++V N+    +  ++R++F  +GE+K +R  P K      H+  
Sbjct: 8   QVPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVR-LPKKMTGTGAHRGF 60

Query: 278 -FIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP 311
            F++F   + A+ A  +L + + + G+R+ LE +  
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 61.6 bits (150), Expect = 7e-12
 Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 8/102 (7%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------TACKHRG 190
           G+   +G+ P  +  +  + VRNI       E+R LF  +G+++T+           HRG
Sbjct: 1   GSSGSSGQVPKKQ-TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59

Query: 191 FVMISYYDIRAARTAMRALQN-KPLRRRKLDIHFSIPKDNPS 231
           F  + +   + A+ A  AL +   L  R+L + ++  +    
Sbjct: 60  FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 8/88 (9%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHK---FIEFYDVRAAEA 289
             L + NL+ S + E L+ +F   G +K       +            F+E+     A+ 
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 290 ALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           ALK L    + G ++++  S       +
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPAS 93

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 8/92 (8%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDI 199
           G   S  LF++N+N +  +  L+ +F + G I        +         GF  + Y   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
             A+ A++ LQ   +   KL++  S     P+
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERATKPA 92

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 66.8 bits (163), Expect = 4e-13
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V ++      +++++ F  YGE+K I     R T   + +  +E+   + A AA ++
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 294 LNRSDIAGKRIKLEPSRPGGARRN 317
           LN ++I G+ I+++     G +R 
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRV 157

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 60.6 bits (147), Expect = 6e-11
 Identities = 20/108 (18%), Positives = 41/108 (37%), Gaps = 5/108 (4%)

Query: 131 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---- 186
           +  V N         P        LFV +I+   ++ E++  F  YG+I+ ++       
Sbjct: 51  YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 110

Query: 187 -KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 233
              +G+ ++ Y   + A  A  AL    +  + + + +   K     K
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK 158

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 65.2 bits (159), Expect = 4e-13
 Identities = 13/89 (14%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
            S  + VR +  +V +++L    E++G I  +      +   ++ + +I +A+  +    
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICYV-MMMPFKRQALVEFENIDSAKECVTFAA 72

Query: 211 NKP--LRRRKLDIHFSIPKDNPSDKDLNQ 237
           + P  +  ++   ++S  K      +   
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 57.9 bits (140), Expect = 1e-10
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            + V  L  SV   DL +    +G +  +   P KR    +EF ++ +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECVTFAADVP 75

Query: 299 --IAGKRIKLEPSR 310
             IAG++     S 
Sbjct: 76  VYIAGQQAFFNYST 89

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 65.2 bits (159), Expect = 5e-13
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 202
           G           +  +N+ +    +E++  F ++G +  +          ++ + +   A
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEA 59

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 233
           R A R L         L + ++ P       
Sbjct: 60  RKAFRHLAYSKFHHVPLYLEWA-PIGVFGAA 89

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 63.3 bits (154), Expect = 3e-12
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            ++  NL       ++++ F  +G +  +   P       +EF +   A  A + L  S 
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVL-LPEGGITAIVEFLEPLEARKAFRHLAYSK 70

Query: 299 IAGKRIKLE 307
                + LE
Sbjct: 71  FHHVPLYLE 79

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 64.5 bits (157), Expect = 6e-13
 Identities = 17/87 (19%), Positives = 30/87 (34%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 285
           P   P +       + V NL       DL++     G V         R   F+ + D  
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSA 67

Query: 286 AAEAALKSLNRSDIAGKRIKLEPSRPG 312
           AA+ A+  L    +    +++  +R  
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 60.6 bits (147), Expect = 2e-11
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 137 GAGTVAGEHP--YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMI 194
            +G+     P   G   +  ++V N+  +   S+L+    + G +    T    R    +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 195 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
            Y D  AA+ A+  LQ   L    L +  +  + +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 64.6 bits (158), Expect = 7e-13
 Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 284
           P+ +  +  T+ V NL       DL+++F  +G +  I     + T   +   FI F+  
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 285 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
             A  A+  ++        + +E ++P     
Sbjct: 68  EDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.8 bits (130), Expect = 4e-09
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
            + T+ V N++ +  +++L+ LF  +G I  +Y A      + +GF  IS++    A  A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           +  +         L++ ++ P  N
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTN 97

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 64.3 bits (157), Expect = 7e-13
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 242 VFNLD-PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 300
           + NL   +VS EDL +IF  YG + +I     K    FI+F + ++   A++  ++    
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIEXESQEMNF 83

Query: 301 GKRIKLEPSRPG 312
           GK++ LE S   
Sbjct: 84  GKKLILEVSSSN 95

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 142 AGEHPYGEHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDI 199
           +G  P G H    LF+ N+   NV   +L  +F  YG I            F  I + + 
Sbjct: 12  SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM----QINIKNAFGFIQFDNP 67

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPK 227
           ++ R A+     +    +KL +  S   
Sbjct: 68  QSVRDAIEXESQEMNFGKKLILEVSSSN 95

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 64.2 bits (157), Expect = 8e-13
 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 5/95 (5%)

Query: 228 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFY 282
              S     +  L V  L   V ++ L   F  +G++ +I      ET   R   F+EF 
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

Query: 283 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
               A AA+ ++N S++ G+ I++  ++P   + +
Sbjct: 63  LAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 53.0 bits (128), Expect = 7e-09
 Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTA 205
             R L+V  +   V+D  L A F  +GDI        Y   KHRGF  + +     A  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSD 232
           +  +    L  R + ++ + P      
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRIKES 97

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 63.8 bits (156), Expect = 9e-13
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEA 289
            L +  L +  L  S + E+L +I  A+G VK++R         +   ++E+ +   A  
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73

Query: 290 ALKSLNRSDIAGKRIKLEPSRPGGAR 315
           A+  ++   I    IK+  S  G + 
Sbjct: 74  AVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAM 206
               LF+  +  +    EL  + + +G ++ L        K +G   + Y +   A  A+
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75

Query: 207 RALQNKPLRRRKLDIHFSIPKDN 229
             +    ++   + +  S    +
Sbjct: 76  MKMDGMTIKENIIKVAISNSGPS 98

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 64.2 bits (157), Expect = 9e-13
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEF 281
           S     P+ +     TL V  L    + E L++ F      + +  RET   +   F++F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDF 61

Query: 282 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
                A+AA +++   +I G ++ L+ ++P G   +
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGS 97

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMR 207
           PS+TLFV+ ++ +  +  L+  F+     R +    T    +GF  + +     A+ A  
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETG-SSKGFGFVDFNSEEDAKAAKE 72

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPS 231
           A+++  +   K+ + ++ PK    
Sbjct: 73  AMEDGEIDGNKVTLDWAKPKGEGG 96

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 64.2 bits (157), Expect = 9e-13
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 283
            P  +     T+ V  LD  VS   L ++F   G V        R T   + + F+EF  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRP 311
              A+ A+K ++   + GK I++  +  
Sbjct: 67  EEDADYAIKIMDMIKLYGKPIRVNKASA 94

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 15/98 (15%), Positives = 39/98 (39%), Gaps = 6/98 (6%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGF 191
           G+   +G      +   T++V  ++  V +  L  LF Q G +   +        +H+G+
Sbjct: 1   GSSGSSG-PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59

Query: 192 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
             + +     A  A++ +    L  + + ++ +   + 
Sbjct: 60  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 97

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 63.8 bits (156), Expect = 1e-12
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 292
           G L V NL  + S EDL ++F AYG + E+       T   +   F+ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 293 SLNRSDIAGKRIKLEPSRPGGARRN 317
            ++     G+ + + PS        
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 59.9 bits (146), Expect = 2e-11
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
            S  LFVRN++    + +L  LF  YG +  L+        K +GF  +++     A  A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSD 232
              +  +  + R L +  S  K   S 
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 63.8 bits (156), Expect = 1e-12
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 231 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAA 290
                   TL V+  D  ++   LR  F  +G + ++   P +    F+ +  + +A+ A
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNC-AFVTYEKMESADQA 65

Query: 291 LKSLNRSDIAGKRIKLEPSRP 311
           +  LN + +   ++K+  +R 
Sbjct: 66  VAELNGTQVESVQLKVNIARK 86

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 196
           G+   +GE         TL+V   +  +  + LR  F  +G+I  L      R    ++Y
Sbjct: 1   GSSGSSGERR-APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTY 56

Query: 197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 230
             + +A  A+  L    +   +L ++ +  +   
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARKQPML 90

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 63.8 bits (156), Expect = 1e-12
 Identities = 21/97 (21%), Positives = 45/97 (46%), Gaps = 3/97 (3%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIE 280
           S      S+       L V N+     + DLRQ+FG +G++ ++    ++R  K   F+ 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           F +   A+ A + L+ + + G++I++  +       +
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAMR 207
             + L V NI     D +LR +F Q+G I     ++     +GF  +++ +   A  A  
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPSDK 233
            L    +  RK++++ +  +   +  
Sbjct: 74  KLHGTVVEGRKIEVNNATARVMTNSG 99

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 64.3 bits (157), Expect = 1e-12
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V  +    + ED+   F  YGE+K I     R T + + +  +E+   + A+AA++ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 294 LNRSDIAGKRIKLEPSRPGGARRN 317
           LN  D+ G+ I ++     G  + 
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPKG 107

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 57.8 bits (140), Expect = 3e-10
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 5/88 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
               LFV  ++    + ++   F +YG+I+ ++          +G+ ++ Y   + A+ A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSDK 233
           M  L  + L  + + + +   +  P  K
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRGPPKGK 108

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 5/94 (5%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 283
             S    ++G L V  L    + + L Q+F  YG++ E+     RET   R   F+ F +
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           +  A+ A+ ++N   + G++I+++ +      R+
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.9 bits (120), Expect = 8e-08
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRA 201
               LFV  ++ +  +  L  +F +YG I    +             RGF  +++ +I  
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQI----SEVVVVKDRETQRSRGFGFVTFENIDD 66

Query: 202 ARTAMRALQNKPLRRRKLDIHFSIPKDN 229
           A+ AM A+  K +  R++ +  +    +
Sbjct: 67  AKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 63.0 bits (154), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSL 294
           G + + NLD S+ N+ L   F A+G +   K + +    + + F+ F    AAE A++ +
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 295 NRSDIAGKRIKLEPSRPGGARR 316
           N   +  +++ +   +    R 
Sbjct: 66  NGMLLNDRKVFVGRFKSRKERE 87

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 52.6 bits (127), Expect = 1e-08
 Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 15/112 (13%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIRAART 204
           S  +F++N++ ++++  L   F  +G+I     +CK        +G+  + +    AA  
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNI----LSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDN----PSDKDLNQGTLVVFNLDPSVSNE 252
           A+  +    L  RK+ +     +         +      + + N  P  +  
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 62.0 bits (151), Expect = 3e-12
 Identities = 9/75 (12%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN 295
               ++V NL    + +++  +   Y    +       +   F+   +   A+ A++  +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 296 RSDIAGKRIKLEPSR 310
           +    GK + ++   
Sbjct: 62  QYSFRGKDLIVQLQP 76

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 58.2 bits (141), Expect = 7e-11
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           G   S  + V+N+  +    E+  L + Y  ++  Y   +++    ++  +   A+ A++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQ 58

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 238
                  R + L +        P+D  L  G
Sbjct: 59  MFHQYSFRGKDLIVQLQ-----PTDALLCSG 84

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V  L   V ++ L   F  +G++ +I      ET   R   F+EF     A AA+ +
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 294 LNRSDIAGKRIK 305
           +N S++ G+ I+
Sbjct: 69  MNESELFGRTIR 80

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
             R L+V  +   V+D  L A F  +GDI  +         KHRGF  + +     A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 206 MRALQNKPLRRRKL 219
           +  +    L  R +
Sbjct: 66  IDNMNESELFGRTI 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           +  L P  +++DL ++   YG++        + T   + + F++F    AA+ A+ +L  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 297 SDIAGKRIKLEPSRPG 312
           S +  +  K      G
Sbjct: 70  SGVQAQMAKQSGPSSG 85

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYD 198
           G   S  L++R +     D +L  L + YG I     + K          +G+  + +  
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKI----VSTKAILDKTTNKCKGYGFVDFDS 56

Query: 199 IRAARTAMRALQNKPLRRRKL 219
             AA+ A+ AL+   ++ +  
Sbjct: 57  PSAAQKAVTALKASGVQAQMA 77

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 63.2 bits (154), Expect = 5e-12
 Identities = 32/130 (24%), Positives = 57/130 (43%), Gaps = 13/130 (10%)

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 252
           ++S YD       ++ LQ +  +         IP    + +      L+V  +  +V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 253 DLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
            LRQ+F  YG ++ +     RET   R + F++F    +A+ A+  LN  +I  KR+K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 308 PSRPGGARRN 317
            +  G  R  
Sbjct: 118 LAASGHQRPG 127

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 46.7 bits (111), Expect = 3e-06
 Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 13/115 (11%)

Query: 133 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK----- 187
                      +        R L V  I + V++ +LR LFE+YG I     + K     
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI----ESVKIVCDR 78

Query: 188 ----HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 238
                RG+  + +    +A+ A+  L    +  ++L +  +             G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG 133

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 62.8 bits (152), Expect = 5e-12
 Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 11/114 (9%)

Query: 222 HFSIPKDNPSDKDLNQGTLV-VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE 280
             + P +       N+  L+ + N    ++ + L  +    G+V+ I           +E
Sbjct: 9   RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVE 68

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKL--EPSRPGGARRNLMLQLNQELEQDESR 332
           F  V  A+ A  +LN +DI      L  E +RP         +LN     ++S 
Sbjct: 69  FESVLCAQKAKAALNGADIYAGCCTLKIEYARPT--------RLNVIRNDNDSW 114

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.1 bits (119), Expect = 1e-07
 Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 149 EHPSRTLF--VRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM 206
              ++ L   ++N    +    L  +    G ++ +    ++    M+ +  +  A+ A 
Sbjct: 20  SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79

Query: 207 RALQNKPL--RRRKLDIHFSIPKD 228
            AL    +      L I ++ P  
Sbjct: 80  AALNGADIYAGCCTLKIEYARPTR 103

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 64.0 bits (155), Expect = 5e-12
 Identities = 29/144 (20%), Positives = 60/144 (41%), Gaps = 12/144 (8%)

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLV-VFNLDPSVSN 251
           M  ++   +A+ A++A+ +       L    +      +    +    + V NL   V+ 
Sbjct: 1   MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60

Query: 252 EDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSDI--AGKRIKLEP 308
           + L QIF  +G V +I         +  +++ D  +A+ A  SL+  +I  A   ++++ 
Sbjct: 61  DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 309 SRPGGARRNLMLQLNQELEQDESR 332
           S+           LN +   D+SR
Sbjct: 121 SKLT--------SLNVKYNNDKSR 136

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 58.2 bits (140), Expect = 5e-10
 Identities = 28/129 (21%), Positives = 49/129 (37%), Gaps = 9/129 (6%)

Query: 132 YSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF 191
               + A   AG    G+ P   + V N+   V    L  +F ++G +  + T  K+  F
Sbjct: 26  ALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 85

Query: 192 -VMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIPKD------NPSDKDLNQGTLVV 242
             ++ Y D  +A+ A  +L  + +      L I FS          N   +D  +  L  
Sbjct: 86  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 145

Query: 243 FNLDPSVSN 251
            +  PS+  
Sbjct: 146 GDSQPSLDQ 154

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V  +    + ED+   F  YGE+K I     R T + + +  +E+   + A+AA++ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 294 LNRSDIAGKRIKLEPSRP 311
           LN  D+ G+ I ++    
Sbjct: 85  LNGQDLMGQPISVDWCFV 102

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
               LFV  ++    + ++   F +YG+I+ ++          +G+ ++ Y   + A+ A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNP 230
           M  L  + L  + + + +   +  P
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVRGPP 106

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 5/85 (5%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 280
                     ++ T+ V NL  S++N DL +IF  YG+V ++     ++T   +   FI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIK 305
           F D  +A+   +++N   + G+ IK
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIK 89

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRG 190
            +G+             T++V N+  ++ +++L  +F +YG +  +       T  K +G
Sbjct: 2   SSGSSGMSGGLAP-SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR-KSKG 59

Query: 191 FVMISYYDIRAARTAMRALQNKPLRRRKL 219
              I + D  +A+   RA+ NK L  R +
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVI 88

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 63.3 bits (154), Expect = 5e-12
 Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 6/103 (5%)

Query: 209 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQG-TLVVFNLDPSVSNEDLRQIFGAYGEVKEI 267
           +    +   +  +         S         L V  L   V ++ L   F  +G++ +I
Sbjct: 34  VAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 268 -----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
                 ET   R   F+EF     A AA+ ++N S++ G+ I+
Sbjct: 94  QIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.2 bits (133), Expect = 4e-09
 Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 135 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHR 189
            +G    +G         R L+V  +   V+D  L A F  +GDI  +         KHR
Sbjct: 46  VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

Query: 190 GFVMISYYDIRAARTAMRALQNKPLRRRKL 219
           GF  + +     A  A+  +    L  R +
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTI 135

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 61.4 bits (150), Expect = 6e-12
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAE 288
           + +  ++ V N+D   + E+L   F   G V  +     + + H +   +IEF D  +  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 289 AALKSLNRSDIAGKRIKLEPSRP 311
            +L  L+ S   G++IK+ P R 
Sbjct: 63  TSLA-LDESLFRGRQIKVIPKRT 84

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 44.8 bits (107), Expect = 4e-06
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAAR 203
           E  +R+++V N++      EL A F   G +  +   C       +GF  I + D  + R
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 204 TAMRALQNKPLRRRKL 219
           T++ AL     R R++
Sbjct: 63  TSL-ALDESLFRGRQI 77

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 61.1 bits (149), Expect = 9e-12
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
           PSR +++ +I  +  + ++  L    G +  L         + +G+  I + D+ ++ +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPSD 232
           +R L    L  R L   +S   D    
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGV 87

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 60.7 bits (148), Expect = 1e-11
 Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           + ++    + E +  +    G V  +      +T   + + FIEF D+ ++ +A+++LN 
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66

Query: 297 SDIAGKRIKLEPSRPGGARRNLMLQLNQE 325
             +  + +K   S         +   +  
Sbjct: 67  YQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 61.1 bits (149), Expect = 1e-11
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 5/91 (5%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHKFIEFYDVR 285
              +      L + NL+P+ S  +L+          ++      T   R   +++F    
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69

Query: 286 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
             E AL+ L    + G  IKLE  +     R
Sbjct: 70  DLEKALE-LTGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 42.2 bits (100), Expect = 5e-05
 Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 205
               LF+ N+N N   +EL+    +        +  + T   +R F  + +        A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TNRKFGYVDFESAEDLEKA 74

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           +  L    +   ++ +     +D 
Sbjct: 75  L-ELTGLKVFGNEIKLEKPKGRDG 97

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 60.6 bits (148), Expect = 1e-11
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V +L  +++ + LR IF  +G++  I      +T   + + FI F D   A  AL+ 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 294 LNRSDIAGKRIKLEPSRPGGARRN 317
           LN  ++AG+ +++          +
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGS 90

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 5/90 (5%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 202
           G   S  L+V +++ N+ +  LR +FE +G I  +         + +G+  I++ D   A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPSD 232
           R A+  L    L  R + +     + +   
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGS 90

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 60.8 bits (148), Expect = 1e-11
 Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 278
           S     PSD      T+ + NL      E L ++   +G++K +      +T H +   F
Sbjct: 3   SGSSGLPSDVT-EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 279 IEFYDVRAAEAALKSLNRS------DIAGKRIKLEPSRPGGARRNL 318
            +F    AA+  L + +         + G+++K++ +       + 
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 54.7 bits (132), Expect = 2e-09
 Identities = 17/99 (17%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIR 200
           P      +T+F+RN++ + E+  L  + +Q+GD++ +           +G     +    
Sbjct: 9   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68

Query: 201 AARTAMRALQNKPLRR------RKLDIHFSIPKDNPSDK 233
           AA+  + A   +          R+L +  ++ +D  +  
Sbjct: 69  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 64.5 bits (156), Expect = 2e-11
 Identities = 21/93 (22%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 151 PSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAART 204
           P+ T+++ N+N  ++  EL+    A+F Q+G I    +  + K RG   + + ++ +A  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 237
           A+R++Q  P   + + I ++    +   K    
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 100

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 60.3 bits (145), Expect = 5e-10
 Identities = 27/160 (16%), Positives = 58/160 (36%), Gaps = 9/160 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALK 292
           T+ + NL+  +  ++L++    IF  +G++ +I    +   R   F+ F +V +A  AL+
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 293 SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQ 352
           S+       K ++++ ++        M     E ++   +       +P T         
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGA 130

Query: 353 FSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 392
                                 +P   +HMPG    + P 
Sbjct: 131 TPVVGAVQGPVP---GMPPMTQAPRIMHHMPGQPPYMPPP 167

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 54.5 bits (130), Expect = 4e-08
 Identities = 14/91 (15%), Positives = 28/91 (30%)

Query: 128 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 187
           G +             +      P+  LF+ N+     +  L  LF Q+   + +     
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRK 218
                 + + +   A  A  ALQ   + +  
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNN 273

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 52.6 bits (125), Expect = 2e-07
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L + NL    +   L  +F  +   KE+R  P +    F+EF +   A AA  +L    
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 299 I-AGKRIKLEPSR 310
           I     +K+  ++
Sbjct: 269 ITQNNAMKISFAK 281

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 23/93 (24%), Positives = 48/93 (51%), Gaps = 6/93 (6%)

Query: 231 SDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 284
           S K+  +G  L +++L     ++DL Q+F  +G V        ++T   +   F+ + + 
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77

Query: 285 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
            +A+AA++S+N   I  KR+K++  R     ++
Sbjct: 78  VSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 45.4 bits (108), Expect = 4e-06
 Identities = 19/116 (16%), Positives = 46/116 (39%), Gaps = 19/116 (16%)

Query: 123 SASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL 182
           S+  +GL   S+        G           LF+ ++     D +L  +F  +G++   
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGP------EGANLFIYHLPQEFGDQDLLQMFMPFGNV--- 52

Query: 183 YTACK---------HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
             + K          + F  +SY +  +A+ A++++    +  ++L +     K++
Sbjct: 53  -VSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.0 bits (146), Expect = 3e-11
 Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNRSD 298
           V N+     + DLRQ+FG +G++ ++    ++R  K   F+ F +   A+ A + L+ + 
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV 93

Query: 299 IAGKRIKLEPSRP 311
           + G++I++  +  
Sbjct: 94  VEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAART 204
            +   + L V NI     D +LR +F Q+G I     ++     +GF  +++ +   A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84

Query: 205 AMRALQNKPLRRRKLDIHFSIPK 227
           A   L    +  RK++++ +  +
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.8 bits (145), Expect = 3e-11
 Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 9/96 (9%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGD-------IRTLYTACKHRGFVMISYYDIRAAR 203
            +  LF+  I    +  E+     +  +         +     K+RGF  + Y   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 204 TAMRALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQ 237
            A R L    ++    ++ + ++ P+ +  +  +  
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 56.0 bits (135), Expect = 8e-10
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 9/85 (10%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV-------KEIRETPHKRHHKFIEFYDVRAAE 288
               L +  +      E++ +      E            +    R   F+E+   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 289 AALKSLNRSD--IAGKRIKLEPSRP 311
            A + L      + G +I ++ + P
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEP 91

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 60.0 bits (146), Expect = 4e-11
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 4/86 (4%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAAL 291
           + G L +  L+   + + L+ +FG +G + E+      T   R   FI F +   A+ A 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 292 KSLNRSDIAGKRIKLEPSRPGGARRN 317
           K +N   + GK IK+E ++    +  
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSG 91

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 50.8 bits (122), Expect = 5e-08
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 12/89 (13%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAA 202
               LF+  +N    +  L+A+F ++G I        RT     K RGF  I++ +   A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT----SKSRGFAFITFENPADA 61

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
           + A + +  K L  + + +  +      S
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 60.1 bits (146), Expect = 4e-11
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 8/107 (7%)

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGE 263
           +  AL   PL    L    +       +    +G  L +++L    ++ DL   F  +G 
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEG--PEGCNLFIYHLPQEFTDTDLASTFLPFGN 66

Query: 264 VKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 305
           V        ++T   +   F+ F +  +A+ A+K++N   +  KR+K
Sbjct: 67  VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 45.1 bits (107), Expect = 7e-06
 Identities = 19/108 (17%), Positives = 47/108 (43%), Gaps = 14/108 (12%)

Query: 121 SDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIR 180
           + + S + L   ++   A   AG+   G      LF+ ++     D++L + F  +G++ 
Sbjct: 10  ASALSTSPLASVALSAAAAAAAGKQIEGPEGCN-LFIYHLPQEFTDTDLASTFLPFGNV- 67

Query: 181 TLYTACK---------HRGFVMISYYDIRAARTAMRALQNKPLRRRKL 219
               + K          + F  +S+ +  +A+ A++A+    +  ++L
Sbjct: 68  ---ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL 112

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 59.3 bits (144), Expect = 4e-11
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 11/85 (12%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRETPHKRHHK-----FIEFYDVRAAEAAL 291
           T+++ N+ P    + +      Y    V  IR    K+  +     F++      A   L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 292 KSLNRSD----IAGKRIKLEPSRPG 312
           + L        I GK I ++ ++  
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 15/94 (15%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD--------IRTLYTACKHRGFVMI 194
           G H    H   T+ +RNI  +     +      Y          I+   T  ++RGF  +
Sbjct: 2   GHHH--HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQ-QNRGFAFV 58

Query: 195 SYYDIRAARTAMRALQNKPLRR----RKLDIHFS 224
                  A   ++ LQ+         + + + F+
Sbjct: 59  QLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 59.5 bits (145), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           V NLD  + +E LR+ F  +G +   K + E    +   F+ F     A  A+  +N   
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 299 IAGKRIKLEPSRPGGARRN 317
           +A K + +  ++    R++
Sbjct: 80  VATKPLYVALAQRKEERQS 98

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 47.6 bits (114), Expect = 7e-07
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 11/81 (13%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIRAARTAMR 207
           L+V+N++  ++D  LR  F  +G I    T+ K        +GF  + +     A  A+ 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTI----TSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73

Query: 208 ALQNKPLRRRKLDIHFSIPKD 228
            +  + +  + L +  +  K+
Sbjct: 74  EMNGRIVATKPLYVALAQRKE 94

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 59.6 bits (145), Expect = 4e-11
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 242 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           V +L  +++ + LR IF  +G ++ I      ET   + + FI F D   A+ AL+ LN 
Sbjct: 31  VGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG 90

Query: 297 SDIAGKRIKLEPSRP 311
            ++AG+ +K+     
Sbjct: 91  FELAGRPMKVGHVTE 105

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 20/99 (20%), Positives = 43/99 (43%), Gaps = 5/99 (5%)

Query: 136 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRG 190
           + A  +A     G      L+V +++ N+ +  LR +FE +G I ++         + +G
Sbjct: 10  HMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG 69

Query: 191 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
           +  I++ D   A+ A+  L    L  R + +     + +
Sbjct: 70  YGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.9 bits (143), Expect = 5e-11
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           ++ V      V +  L + F A+G V  +     K     +E  DV A EA L   ++  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68

Query: 299 IAGKRIKLEPSRP 311
           + G R+++ P   
Sbjct: 69  LGGHRLRVRPREQ 81

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           G    R++FV      V+ ++L   F  +G + ++        F ++   D+ A    + 
Sbjct: 4   GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL- 62

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPSDK 233
           +     L   +L +     K+  S  
Sbjct: 63  SQSQHSLGGHRLRVRPREQKEFQSPA 88

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 58.6 bits (142), Expect = 7e-11
 Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 2/71 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK--FIEFYDVRAAEAALKSLNR 296
            L + N+ P +  E L  +   YG V+   +           + +     A  AL  LN 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76

Query: 297 SDIAGKRIKLE 307
             +    +K+ 
Sbjct: 77  FQLENFTLKVA 87

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 3/93 (3%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR--GFVMI 194
           G+   +G  P  +   R L +RNI  +++   L +L  QYG + +            V +
Sbjct: 1   GSSGSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59

Query: 195 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 227
           +Y     AR A+  L    L    L + +   +
Sbjct: 60  TYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSL 294
             + V NL    + + L+  F   G V       E    +    ++F     AE A + +
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68

Query: 295 NRSDIAGKRIKLEPSRPGGARRN 317
           N   ++G+ I +   R      +
Sbjct: 69  NGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 11/91 (12%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIR 200
           G   +  +FVRN+  +     L+  F + G +                +G  ++ +    
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHV----LYADIKMENGKSKGCGVVKFESPE 59

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
            A  A R +    L  R++D+        PS
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDRNASGPS 90

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 57.4 bits (139), Expect = 3e-10
 Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 278
           S           N   + V +L P ++ ED++  F  +G + +        T   + + F
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           + F++   AE A++ +    + G++I+   +        
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPK 100

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 47.7 bits (114), Expect = 7e-07
 Identities = 15/108 (13%), Positives = 44/108 (40%), Gaps = 7/108 (6%)

Query: 138 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGF 191
             + +            +FV +++  +   +++A F  +G       ++ + T  K +G+
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG-KSKGY 59

Query: 192 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 239
             +S+++   A  A++ +  + L  R++  +++  K           T
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 56.4 bits (137), Expect = 3e-10
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           +L+ +V +E LR  F  +            +T   R + F+ F     A+ A+ S+   D
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67

Query: 299 IAGKRIKLEPSRP 311
           + G+ +++  +  
Sbjct: 68  LNGRPLRINWAAK 80

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 50.2 bits (121), Expect = 5e-08
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAARTA 205
           +  LFV ++N NV+D  LR  F+ +        +  + T    RG+  +S+     A+ A
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG-SSRGYGFVSFTSQDDAQNA 59

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           M ++Q + L  R L I+++   ++
Sbjct: 60  MDSMQGQDLNGRPLRINWAAKLEH 83

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
           ++ V N+    + E L+ IF   G V        RET   + + F E+ D   A +A+++
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 294 LNRSDIAGKRIKLEPSRPGGARR 316
           LN  + +G+ ++++ +     + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKE 92

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 56.1 bits (136), Expect = 7e-10
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 6/99 (6%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIR 200
           P  +   R++FV NI     + +L+ +F + G + +          K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPKDN-PSDKDLNQG 238
            A +AMR L  +    R L +  +  + N    K L  G
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR--HHK---FIEFYDVRAAEAALKS 293
           T+ V NL+  V  E L ++F   G + ++      R    K   F+ F    +   A+  
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVT-ICKDREGKPKSFGFVCFKHPESVSYAIAL 76

Query: 294 LNRSDIAGKRIK 305
           LN   + G+ I 
Sbjct: 77  LNGIRLYGRPIN 88

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFV 192
           G+   +G  P  E   RT+FV N+ + V +  L  LF Q G +  +        K + F 
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKL 219
            + +    +   A+  L    L  R +
Sbjct: 61  FVCFKHPESVSYAIALLNGIRLYGRPI 87

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 56.0 bits (136), Expect = 4e-10
 Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           +L P ++   +   F  +G + + R      T   + + F+ F++   AE A++ +    
Sbjct: 13  DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72

Query: 299 IAGKRIKLEPSRP 311
           + G++I+   +  
Sbjct: 73  LGGRQIRTNWATR 85

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 14/83 (16%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAART 204
               +FV +++  +  + + A F  +G       ++ + T  K +G+  +S+++   A  
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATG-KSKGYGFVSFFNKWDAEN 63

Query: 205 AMRALQNKPLRRRKLDIHFSIPK 227
           A++ +  + L  R++  +++  K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 57.0 bits (138), Expect = 5e-10
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 13/86 (15%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKFIEFYDVR 285
           T+ V  L  +V+ E +   F   G +K               RET   +    + F D  
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 286 AAEAALKSLNRSDIAGKRIKLEPSRP 311
           +A+AA+   +  + +G  IK+  +  
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATR 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.3 bits (136), Expect = 7e-10
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 13/96 (13%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRT----------LYT---ACKHRGFVMISYY 197
            + T+FV+ +  NV    +   F+Q G I+T          LYT     K +G   +S+ 
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 198 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 233
           D  +A+ A+     K      + + F+  + + +  
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.5 bits (137), Expect = 6e-10
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 237 QGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAAL 291
             T L + NL  S+  ++L  +   +G+V   R     +   R   F         EA +
Sbjct: 24  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 292 KSLNRSDIAGKRIKLEPSRP 311
              N   I        P+ P
Sbjct: 84  GHFNGKFIKTPPGVSAPTEP 103

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.9 bits (107), Expect = 7e-06
 Identities = 10/90 (11%), Positives = 27/90 (30%), Gaps = 17/90 (18%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDIRAARTAM 206
           L++ N+  ++++ EL  + + +G +     + +         RG               +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQV----ISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 207 RALQNKPLRRRKLDIHFSIPK-----DNPS 231
                K ++        + P         S
Sbjct: 84  GHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.9 bits (135), Expect = 7e-10
 Identities = 11/89 (12%), Positives = 33/89 (37%), Gaps = 5/89 (5%)

Query: 233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDVRAAE 288
            D+   ++ +       + +D+++     G+V  I+      +  K   F+ F  + +A+
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 289 AALKSLNRSDIAGKRIKLEPSRPGGARRN 317
             ++           + +       A++N
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDDYFAKKN 94

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.7 bits (106), Expect = 7e-06
 Identities = 8/77 (10%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAART 204
           +  +R+++++   ++    +++   E  G +  +          +G + + +  I +A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 205 AMRALQNKPLRRRKLDI 221
            +     +  +   L I
Sbjct: 68  FV-ETPGQKYKETDLLI 83

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 56.3 bits (136), Expect = 7e-10
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 13/101 (12%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RET 270
           S       D+D +   + V  L+ SV+ +DL   F   G VK               +ET
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 271 PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
              +    + + D   A+AA++  +  D  G ++K+  +R 
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 49.3 bits (118), Expect = 2e-07
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 13/93 (13%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-------------RGFVMISYYD 198
           +  ++V+ +N +V   +L   F+Q G ++      +              +G   +SY D
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 199 IRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
              A+ A+     K  +  KL +  +  K   +
Sbjct: 75  PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEA 289
               + + NLDP +  + L   F A+G + +        +T + + + FI F    A++A
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 290 ALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           A++++N   +  + I +  +    ++ +
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 14/92 (15%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----------RGFVMISYY 197
           G   S  +F+ N++  +++  L   F  +G I                   +G+  I++ 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFA 56

Query: 198 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
              A+  A+ A+  + L  R + + ++  KD+
Sbjct: 57  SFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 88

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            + V NL  S ++E ++++F  +G+V  +     RET   +   F+E  +  +   A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 294 LNRSDIAGKRIKLEPSRPGGARRN 317
           L+ +D  G+ I++  + P  +  +
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEH 85

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 45.2 bits (108), Expect = 3e-06
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 207
           R ++V N+  +    +++ LF Q+G +  +         K +GF  +   +  +   A+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPSDKD 234
            L N     R + +  + PK +     
Sbjct: 61  KLDNTDFMGRTIRVTEANPKKSLEHHH 87

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 5/91 (5%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 280
                S        + V N+  +VS +++   F  Y  +       +           + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           F     A AA+  LN   I  +++KL     
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 5/94 (5%)

Query: 139 GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVM 193
            + +     G+     + V+N+   V   E+   F  Y  I        +      G  M
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 194 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 227
           +++     A  A+  L ++P+  RK+ +      
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 13/95 (13%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH---------- 276
             +      +  T+ V  L  +V+ E +   F   G +K  ++T     +          
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 277 K---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 308
           K    + F D  +A+AA+   +  + +G  IK+  
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 13/82 (15%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-------------RGFVMISYY 197
            + T+FV+ +  NV    +   F+Q G I+T     +              +G   +S+ 
Sbjct: 12  DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71

Query: 198 DIRAARTAMRALQNKPLRRRKL 219
           D  +A+ A+     K      +
Sbjct: 72  DPPSAKAAIDWFDGKEFSGNPI 93

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 5/92 (5%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 280
                S        + V N+  +VS +++   F  Y  +       +           + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 312
           F     A AA+  LN   I  +++KL     G
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 50.8 bits (122), Expect = 4e-08
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 138 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFV 192
             + +     G+     + V+N+   V   E+   F  Y  I        +      G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFS 224
           M+++     A  A+  L ++P+  RK+ +   
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 54.5 bits (131), Expect = 3e-09
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 3/69 (4%)

Query: 239 TLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           +LVV N  L   VS   L  +    G V  +   P+K  + F  +     ++ A  +LN 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNG 85

Query: 297 SDIAGKRIK 305
            ++     +
Sbjct: 86  KEVVDDLGQ 94

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.4 bits (128), Expect = 7e-09
 Identities = 13/90 (14%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 149 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM 206
            + +++L V N  + + V  ++L  + E+ G +  L     ++ +    Y     ++ A 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAY 80

Query: 207 RALQNK---PLRRRKLDIHFSIPKDNPSDK 233
             L  K       +K+ ++ +  +      
Sbjct: 81  VTLNGKEVVDDLGQKITLYLNFVEKVQWSG 110

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 53.9 bits (129), Expect = 3e-09
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
           S  L ++N+ + ++   LR L  Q+G + + +      G  +  Y     A  A  AL N
Sbjct: 7   SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-GIALCKYTTREEANKAQMALNN 65

Query: 212 KPLRRRKLDIHFSIPKDNPSDKDLNQ 237
             L    +          PS+ ++  
Sbjct: 66  CVLANTTIFAES------PSENEVQS 85

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 54.6 bits (131), Expect = 4e-09
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSD 298
           ++V NL   V+ + L QIF  +G V +I         +  +++ D  +A+ A  SL+  +
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90

Query: 299 I--AGKRIKLEPSRP 311
           I  A   ++++ S+ 
Sbjct: 91  IYNACCTLRIDFSKL 105

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.8 bits (121), Expect = 8e-08
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 7/102 (6%)

Query: 132 YSVPNGAGTVAGEHPYGEHPSRTLF--VRNINSNVEDSELRALFEQYGDIRTLYTACKHR 189
               + A   AG        S  L   V N+   V    L  +F ++G +  + T  K+ 
Sbjct: 8   ALAASAAAVDAGMAM--AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN 65

Query: 190 GF-VMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIPKD 228
            F  ++ Y D  +A+ A  +L  + +      L I FS    
Sbjct: 66  QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 244 NLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           NL    ++EDL +   + G  ++ EI     R     +    +      +++  +  L +
Sbjct: 8   NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67

Query: 297 SDIAGKRIKLEPSRPGGARRN 317
            ++ G+   + PS       +
Sbjct: 68  RELHGQNPVVTPSNKLEHHHH 88

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 155 LFVRNINSNVEDSELRALFEQYG-----DIRTLY---TACKHRGFVMISYYDIRAARTAM 206
           L++ N+     D +L       G     +I+         + +GF ++      +++  M
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG-QSKGFALVGVGSEASSKKLM 62

Query: 207 RALQNKPLRRRKLDIHFSIPKD 228
             L  + L  +   +  S   +
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLE 84

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 55.2 bits (133), Expect = 5e-09
 Identities = 20/122 (16%), Positives = 41/122 (33%), Gaps = 5/122 (4%)

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 259
                     + KPL  +     F          +     L+V NLD  VS+ D++++F 
Sbjct: 52  GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVE-TGAKLLVSNLDFGVSDADIQELFA 110

Query: 260 AYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 315
            +G +K+       +        + F     A  A+K      + G+ + ++        
Sbjct: 111 EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170

Query: 316 RN 317
            +
Sbjct: 171 EH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LYTAC-KHRGFVMISYYDIRA 201
             G      L V N++  V D++++ LF ++G ++     Y    +  G   + +     
Sbjct: 82  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 141

Query: 202 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 237
           A  AM+  +  PL  R +DI     + +      + 
Sbjct: 142 ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 53.9 bits (130), Expect = 5e-09
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 294
            L+V NLD  VS+ D++++F  +G +K+       +        + F     A  A+K  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96

Query: 295 NRSDIAGKRIKLEPSRPGGARR 316
               + G+ + ++         
Sbjct: 97  KGVPLDGRPMDIQLVASQIDLE 118

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 48.1 bits (115), Expect = 7e-07
 Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 12/98 (12%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 199
           G      L V N++  V D++++ LF ++G +                  G   + +   
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVDYDRSGRSLGTADVHFERR 86

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 237
             A  AM+  +  PL  R +DI     + +      + 
Sbjct: 87  ADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 53.4 bits (129), Expect = 6e-09
 Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 5/102 (4%)

Query: 211 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 268
           ++P +      H            +  G  L+V NLD  VS+ D++++F  +G +K+   
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 269 ---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
               +        + F     A  A+K  N   + G+ + ++
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 44.6 bits (106), Expect = 7e-06
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 199
           G      L V N++  V D++++ LF ++G +                  G   + +   
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVHYDRSGRSLGTADVHFERK 80

Query: 200 RAARTAMRALQNKPLRRRKLDIHF 223
             A  AM+     PL  R ++I  
Sbjct: 81  ADALKAMKQYNGVPLDGRPMNIQL 104

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 55.9 bits (134), Expect = 9e-09
 Identities = 21/113 (18%), Positives = 43/113 (38%), Gaps = 11/113 (9%)

Query: 216 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSN---------EDLRQIFGAYGEVKE 266
           R K   +        S +  N+ TL V  +D ++++           +R +F   G++  
Sbjct: 114 REKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDR 172

Query: 267 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 319
           IR     ++  F++F     AE A ++++   +     K    R  G    + 
Sbjct: 173 IR-YVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVK 224

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.4 bits (117), Expect = 1e-06
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 12/98 (12%)

Query: 143 GEHPYGEHPSRTLFVRNINSNV---------EDSELRALFEQYGDIRTL-YTACKHRGFV 192
           G        ++TL+V  I+  +          +S +R +F + GDI  + Y   K+ GFV
Sbjct: 125 GGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFV 184

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 230
              +     A  A  A+ N+ L            +   
Sbjct: 185 --KFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.8 bits (127), Expect = 9e-09
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 11/88 (12%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNE-------DLRQIFGAYGEVKEI---RETPHKRHH 276
           KD P + D     +VV N+ P V  +        + +IF  +G++       E    + +
Sbjct: 5   KDRPQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGY 63

Query: 277 KFIEFYDVRAAEAALKSLNRSDIAGKRI 304
            F+E+     A  A+K+ +   +  +  
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHT 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.0 bits (99), Expect = 6e-05
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 9/75 (12%)

Query: 149 EHPSRTLFVRNINSNVEDSE------LRALFEQYGDIRTLYTAC---KHRGFVMISYYDI 199
           +     + V N+     D        +  +F ++G I   +      K +G++ + Y   
Sbjct: 12  DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP 71

Query: 200 RAARTAMRALQNKPL 214
             A  A++      L
Sbjct: 72  AHAVDAVKNADGYKL 86

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 12/83 (14%)

Query: 237 QGTLV-VFNLDPSVSNEDL---RQIFGAYGEVKEI-----RETPHKRHHK---FIEFYDV 284
           Q  LV V  L   +++ ++    + FG +G++ ++           +      ++ +   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 285 RAAEAALKSLNRSDIAGKRIKLE 307
             A  A++ +N   + G+ +K  
Sbjct: 74  EDALRAIQCVNNVVVDGRTLKAS 96

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.5 bits (92), Expect = 5e-04
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 11/85 (12%)

Query: 154 TLFVRNINSNVEDSEL---RALFEQYGDI-------RTLYTACK-HRGFVMISYYDIRAA 202
            +FV  ++  + D E+      F ++G I        T Y   +       ++Y     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPK 227
             A++ + N  +  R L       K
Sbjct: 77  LRAIQCVNNVVVDGRTLKASLGTTK 101

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGE----VKEIR--ETPHKRHHKFIEFYDVRAAEAALK 292
           +L + +L+P +    + + F   GE    VK IR   T     + F+EF D+  AE  L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 293 SLNRSDIAG----KRIKL 306
            +N   + G    KR KL
Sbjct: 71  KINGKPLPGATPAKRFKL 88

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 13/82 (15%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGD-------IRTLYTACKHRGFVMISYYDIRAAR 203
            + +L++ ++   ++++ +   F   G+       IR   T     G+  + + D+  A 
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTG-IPAGYCFVEFADLATAE 66

Query: 204 TAMRALQNKPLRRRKLDIHFSI 225
             +  +  KPL        F +
Sbjct: 67  KCLHKINGKPLPGATPAKRFKL 88

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.4 bits (126), Expect = 2e-08
 Identities = 11/93 (11%), Positives = 30/93 (32%), Gaps = 6/93 (6%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----F 278
           S       D +  +    + N+  S++  D+ Q        +         + +      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           ++F +   A  + + L+R  + G+   +     
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTL 93

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYG----DIRTLYTAC-KHRGFVMISYYDIRAA 202
                    + NI  ++   ++    E        +  L     +  G  ++ + +   A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKD 228
           R + R L  K L  R+  +H    +D
Sbjct: 71  RKSER-LHRKKLNGREAFVHVVTLED 95

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 294
           T+ V NLD  V  + L+++F   G V        +    R    + F     A  A+   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 295 NRSDIAGKRIKLEPSRPGGARRN 317
           N   +  + + ++       + +
Sbjct: 77  NGQLLFDRPMHVKMDERALPKGD 99

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.4 bits (108), Expect = 4e-06
 Identities = 17/100 (17%), Positives = 33/100 (33%), Gaps = 13/100 (13%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------H 188
           G+   +G    G     T+FV N++  V   +L+ +F   G +                 
Sbjct: 1   GSSGSSGALQAGR-LGSTVFVANLDYKVGWKKLKEVFSMAGVV----VRADILEDKDGKS 55

Query: 189 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 228
           RG   +++     A  A+     + L  R + +       
Sbjct: 56  RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL 95

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
            +D  +   ++R  F  YG VKE++     T   + + F+ FY+    +  ++  ++ + 
Sbjct: 16  GIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINF 73

Query: 300 AGKRIKLEPSRP 311
            GK++KL P+  
Sbjct: 74  HGKKLKLGPAIR 85

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 49.9 bits (120), Expect = 9e-08
 Identities = 23/103 (22%), Positives = 48/103 (46%), Gaps = 7/103 (6%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRA 201
           P G+    T+FV  I+  ++++E+R+ F +YG ++ +          +G+  +S+Y+   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62

Query: 202 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFN 244
            +  +          +KL +  +I K N S     Q   ++FN
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPAIRKQNLSTYH-VQPRPLIFN 102

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 14/98 (14%), Positives = 33/98 (33%), Gaps = 6/98 (6%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 280
            +            + +  L     N+ +   F     V++     +  + K     F+E
Sbjct: 14  KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
           F +    +AAL   ++  +  + I++ P    G    +
Sbjct: 74  FRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKI 110

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 39.1 bits (91), Expect = 8e-04
 Identities = 16/106 (15%), Positives = 38/106 (35%), Gaps = 15/106 (14%)

Query: 137 GAGTVAGEHPYGEHPSR---------TLFVRNINSNVEDSELRALFEQYG----DIRTLY 183
           G+   +G+ P G+  SR          ++++ +    E+  +   F++       I   Y
Sbjct: 1   GSSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY 60

Query: 184 TAC-KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 228
               K  G   + + +    + A+     + +  R + +H    K 
Sbjct: 61  GPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 105

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 51.2 bits (123), Expect = 3e-08
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 8/94 (8%)

Query: 142 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 196
           +G     +H +  LF+  I  N+++ +L+ LFE++G I  L          H+G   ++Y
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

Query: 197 YDIRAARTAMRALQNK---PLRRRKLDIHFSIPK 227
            +  +A  A  AL  +   P   R + +  +  +
Sbjct: 63  CERESALKAQSALHEQKTLPGMNRPIQVKPADSE 96

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 46.6 bits (111), Expect = 2e-06
 Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 284
              KD +   L +  +  ++  +DL+ +F  +G++ E+     R T   +   F+ + + 
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 285 RAAEAALKSLN 295
            +A  A  +L+
Sbjct: 66  ESALKAQSALH 76

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK------FIEFYDVRAAEAALK 292
           T  + NL   V+ E +++ F     +  +R      + +      + EF D+ +  +AL 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 293 SLNRSDIAGKRIKLEPSRPGGARRN 317
            LN   +  KRI+++ +     + +
Sbjct: 76  -LNEESLGNKRIRVDVADQAQDKDS 99

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 13/97 (13%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 138 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFV 192
             + +      + P  T F+ N+  +V +  ++  F           R      + +GF 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
              + D+ +  +A+ +L  + L  +++ +  +    +
Sbjct: 61  YAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD 96

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 55.2 bits (132), Expect = 5e-08
 Identities = 25/113 (22%), Positives = 47/113 (41%), Gaps = 7/113 (6%)

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 259
              +   +  + +     +L +    P ++P+ +     TL V  ++   +   LR+ F 
Sbjct: 67  MERKRREKIERRQQEVETELKMW--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 260 AYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
            YG +K I     KR  K     FIE+   R   +A K  +   I G+R+ ++
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 47.9 bits (113), Expect = 1e-05
 Identities = 28/133 (21%), Positives = 48/133 (36%), Gaps = 7/133 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
             +TLFV  +N +  +S+LR  FE YG I+ ++        K RG+  I Y   R   +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 206 MRALQNKPL--RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 263
            +    K +  RR  +D+           + L  G          V+     +   +  +
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

Query: 264 VKEIRETPHKRHH 276
            +        R  
Sbjct: 221 ERPGPSPLPHRDR 233

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 10/88 (11%)

Query: 229 NPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYD 283
           + S+    +   L V  L+   S ED+ ++F  +G + E           +   F++F  
Sbjct: 6   SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSS 65

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRP 311
              A+AA+ +L+     G +     S  
Sbjct: 66  HTEAQAAIHALH-----GSQTMPGASSS 88

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 50.4 bits (121), Expect = 6e-08
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 10/97 (10%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAART 204
               R LFV  +N    + ++  LF+ +G I             +G   + +     A+ 
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 205 AMRALQNK---PLRRRKLDIHFSIPKDNPSDKDLNQG 238
           A+ AL      P     L + F+   D   +   + G
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFA---DTDKESGPSSG 105

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 51.8 bits (124), Expect = 5e-08
 Identities = 17/97 (17%), Positives = 33/97 (34%), Gaps = 4/97 (4%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFY 282
                + +      + +  L    +  D+   F     V+  I   P  R      +EF 
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFA 94

Query: 283 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 319
               A AA+   +R+++  + I+L  +   GA     
Sbjct: 95  THEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAY 130

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 50.7 bits (121), Expect = 5e-08
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 149 EHPSRTLFVRNI-NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           +   R + + N+ +S   DS +  L E YG I+      + +    I       A   + 
Sbjct: 22  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVD 80

Query: 208 ALQNKP--LRRRKLDIHFS 224
               K    + R + +  S
Sbjct: 81  HCLKKALWFQGRCVKVDLS 99

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 239 TLVVFNL-DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLN 295
            + + NL     S+  + ++   YG++K       K    FIE      A A +      
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS-QAFIEMETREDAMAMVDHCLKK 85

Query: 296 RSDIAGKRIKLEPSR 310
                G+ +K++ S 
Sbjct: 86  ALWFQGRCVKVDLSE 100

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 51.4 bits (123), Expect = 5e-08
 Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----F 278
            + + + S    N G + +  L    + E++ Q F     V      P     K     F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           ++F     AE AL   ++  I  + I++  S  
Sbjct: 89  VQFASQELAEKALG-KHKERIGHRYIEVFKSSQ 120

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 12/101 (11%), Positives = 30/101 (29%), Gaps = 6/101 (5%)

Query: 133 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-----LYTACK 187
           S+  G     G +         + +R +       E+   F     +       +    K
Sbjct: 23  SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 228
             G   + +     A  A+     + +  R +++  S  ++
Sbjct: 83  ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQEE 122

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 50.8 bits (122), Expect = 7e-08
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 6/97 (6%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 280
              + S KD     + V  L    ++  LR+ F  +G+++E      R+T   R + F+ 
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
             D  AAE A K  N   I G++  +  +  G   R+
Sbjct: 66  MADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRS 101

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 50.4 bits (121), Expect = 7e-08
 Identities = 25/121 (20%), Positives = 43/121 (35%), Gaps = 17/121 (14%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------K 187
            +G+        +     +FV  +  +  D+ LR  FE +GDI                K
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI----EEAVVITDRQTGK 57

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 247
            RG+  ++  D  AA  A +   N  +  RK +++ +     P      Q    +    P
Sbjct: 58  SRGYGFVTMADRAAAERACKDP-NPIIDGRKANVNLAYLGAKPRS---LQTGFAIGVSGP 113

Query: 248 S 248
           S
Sbjct: 114 S 114

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.1 bits (120), Expect = 8e-08
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 231 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVR 285
           S    N G + +  L    S E++ Q F     V      P     +     F++F    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 286 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
            AE ALK  ++  I  + I++  S     R 
Sbjct: 69  IAEKALK-KHKERIGHRYIEIFKSSRAEVRT 98

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.1 bits (122), Expect = 1e-07
 Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAAL 291
            + V +     +++ L Q+  + G  +V E+     R     + +  +      +    L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 292 KSLNRSDIAGKRIKLEPSRP 311
           + L    + G+++ + P+  
Sbjct: 117 ELLPGKVLNGEKVDVRPATR 136

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.1 bits (109), Expect = 5e-06
 Identities = 11/104 (10%), Positives = 32/104 (30%), Gaps = 7/104 (6%)

Query: 135 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-------K 187
            N    +   +    +    ++V + +    D +L  +    G    +           +
Sbjct: 38  NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ 97

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
            +G+  +      +    +  L  K L   K+D+  +  ++   
Sbjct: 98  SKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 49.6 bits (118), Expect = 1e-07
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHHK--FIEFYDVRAAEAALK 292
            + V N+D  +S ++L+Q+    F  +G+VK +  +PH  +     ++  +++ A  A+ 
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70

Query: 293 SLNRSDIAGKRIKLEPSRPGGAR 315
           SL+R  I  K+I +  +      
Sbjct: 71  SLHRYKIGSKKILVSLATGASGP 93

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 5/72 (6%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 292
           G  V+ +    V  + L  +F   G+V  +       T   +   F+E   +  A+  +K
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 293 SLNRSDIAGKRI 304
           S +   +  K  
Sbjct: 73  SFHGKRLDLKHR 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 156 FVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRALQ 210
            + +    V    L +LF + G +  +         K +GF+ +    +  A+  +++  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 211 NKPL 214
            K L
Sbjct: 76  GKRL 79

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 48.6 bits (116), Expect = 3e-07
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            +VV  L PS S +DL+      G+V       ++     +EF        A++ L+ + 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAVRKLDNTK 74

Query: 299 IAGKRIKLEPSRP 311
                 +    R 
Sbjct: 75  FRSHEGETAYIRV 87

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 5/82 (6%)

Query: 145 HPYGEHPSRT---LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRA 201
              G    R+   + V  +  +    +L+    + GD+   Y      G  ++ +     
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKED 62

Query: 202 ARTAMRALQNKPLRRRKLDIHF 223
              A+R L N   R  + +  +
Sbjct: 63  MTYAVRKLDNTKFRSHEGETAY 84

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 11/85 (12%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK------FIEFYDVRAAEAALK 292
           T  + NL   V+ E +++ F     +  +R      + +      + EF D+ +  +AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 293 SLNRSDIAGKRIKLEPSRPGGARRN 317
            LN   +  +RI+++ +      ++
Sbjct: 80  -LNEESLGNRRIRVDVADQ---AQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 14/92 (15%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY---TACKHRGFVMISYY 197
                 + P  T F+ N+  +V +  ++  F       +R         + +GF    + 
Sbjct: 10  HRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 69

Query: 198 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
           D+ +  +A+ +L  + L  R++ +  +    +
Sbjct: 70  DLDSLLSAL-SLNEESLGNRRIRVDVADQAQD 100

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 48.3 bits (115), Expect = 4e-07
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            +VV  L PS S +DL+      G+V       ++     +EF        A++ L+ + 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD--VYRDGTGVVEFVRKEDMTYAVRKLDNTK 75

Query: 299 IAGKRIKLEPSRP 311
                 +    R 
Sbjct: 76  FRSHEGETAYIRV 88

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 2/87 (2%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 196
           G        P        + V  +  +    +L+    + GD+   Y      G  ++ +
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEF 58

Query: 197 YDIRAARTAMRALQNKPLRRRKLDIHF 223
                   A+R L N   R  + +  +
Sbjct: 59  VRKEDMTYAVRKLDNTKFRSHEGETAY 85

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 50.5 bits (120), Expect = 6e-07
 Identities = 18/152 (11%), Positives = 43/152 (28%), Gaps = 13/152 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAAL 291
            L + NL    ++EDL +   + G  ++ EI     R     +    +      +++  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 292 KSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWV 351
             L + ++ G+   + P       +       +   +  ++  Q             +  
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQ------FEMQSRKTTQSGQMSGEGKAGPPGGSSRA 183

Query: 352 QFSSPIEHNPLQTISKSPNFRNMSPTTSNHMP 383
            F            +     R   P      P
Sbjct: 184 AFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPP 215

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 47.4 bits (112), Expect = 6e-06
 Identities = 14/111 (12%), Positives = 33/111 (29%), Gaps = 7/111 (6%)

Query: 135 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYTAC-----K 187
             G G               L++ N+     D +L       G  DI  +         +
Sbjct: 51  DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 238
            +GF ++      +++  M  L  + L  +   +     +     +  ++ 
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 47.1 bits (112), Expect = 1e-06
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK--FIEF 281
               P   + +   + V  +  S    D+R  F     V  +   +    R++    ++F
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKF 63

Query: 282 YDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
              +    ALK  NR  +  + +++ P+  
Sbjct: 64  LSPQDTFEALK-RNRMLMIQRYVEVSPATE 92

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.4 bits (122), Expect = 1e-06
 Identities = 47/440 (10%), Positives = 112/440 (25%), Gaps = 147/440 (33%)

Query: 23  MGLGR-QSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRG 81
           + L    S + +   L K+ + +  +            +++      + A +      + 
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPN----WTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242

Query: 82  LPSSLEDLED------YDIFGSGGGMELEGEPQESLSMSMSKI-------SISDSASGNG 128
             + L  L +      ++ F                     KI        ++D  S   
Sbjct: 243 YENCLLVLLNVQNAKAWNAFNLS-----------------CKILLTTRFKQVTDFLSAAT 285

Query: 129 LLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 188
             H S+                  ++L ++ ++   +D     L  +             
Sbjct: 286 TTHISL------DHHSMTLTPDEVKSLLLKYLDCRPQD-----LPRE---------VLTT 325

Query: 189 RGFV--MIS--------------YYDIRAARTAMRA-LQN-KPLRRRKLDIHFSI-PKDN 229
                 +I+              + +     T + + L   +P   RK+    S+ P   
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385

Query: 230 --PSDKDLNQGTLVVF--NLDPSV-----------------SNEDLRQIFGAYGEVKEIR 268
             P+        L +   ++  S                    E    I   Y E+K   
Sbjct: 386 HIPTI------LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439

Query: 269 ETPHKRHHKFIEFYDV--------------------------RAAEAALKS-------LN 295
           E  +  H   ++ Y++                          +  E   +        L+
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499

Query: 296 RSDIAGK-RIKLEPSRPGGARRNLMLQLN------QELEQDESRILQ------HQVGSPI 342
              +  K R         G+  N + QL        + +    R++        ++   +
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENL 559

Query: 343 TNSPPGNWVQFSSPIEHNPL 362
             S   + ++ +   E   +
Sbjct: 560 ICSKYTDLLRIALMAEDEAI 579

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.5 bits (117), Expect = 4e-06
 Identities = 47/396 (11%), Positives = 96/396 (24%), Gaps = 133/396 (33%)

Query: 458 VETLSGP--QFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQ 515
           VE +     +FL    S        P+  T                 Y  ++      +Q
Sbjct: 83  VEEVLRINYKFLM---SPIKTEQRQPSMMTRM---------------YIEQRDRLYNDNQ 124

Query: 516 ---HHHVGSAPSGVPLER-RFGFLPESPETSFMNPVAFCGM-GIG--------------- 555
               ++V       P  + R   L   P  +    V   G+ G G               
Sbjct: 125 VFAKYNV---SRLQPYLKLRQALLELRPAKN----VLIDGVLGSGKTWVALDVCLSYKVQ 177

Query: 556 --QNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPAN 613
              +   F +N+ +  S    + + + L             ++ P +     +       
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLY-----------QIDPNWTSRSDHSSNIKLR 226

Query: 614 IEGLYERGR----SRRIEN------------------------------NNGNQLDSKKQ 639
           I  +    R    S+  EN                                 + L +   
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286

Query: 640 FQLELEKIRSGEDTRTTLMI---------KNIPN--KYTSKMLLAAIDE---NHKGTYDF 685
             + L+             +         +++P     T+   L+ I E   +   T+D 
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346

Query: 686 LYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAF----NGKK---------WEKFNSEKVA 732
            +  ++      +  + +N+L P      ++                   W       V 
Sbjct: 347 -WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405

Query: 733 SLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHS 768
            +           V      SL+ +  +   I   S
Sbjct: 406 VV-----------VNKLHKYSLVEKQPKESTISIPS 430

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
           T  V NL  +    D+  IF     ++ +R     +T   +   ++EF +V + + AL  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 294 LNRSDIAGKRIKLEPSRPGGARRN 317
            + + +  + ++++ +      ++
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKS 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 39.2 bits (92), Expect = 6e-04
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY---TACKHRGFVMISYYDIRAARTA 205
           P  T +V N+  N    ++ A+F+      +R +    T  K +GF  + + ++ + + A
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTD-KFKGFCYVEFDEVDSLKEA 72

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           +       L  R L +  +  +  
Sbjct: 73  L-TYDGALLGDRSLRVDIAEGRKQ 95

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 11/76 (14%)

Query: 239 TLVVFNLDPSVSNE-------DLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAE 288
            +VV N+ P V  +        + +IF  +G++       E    + + F+E+     A 
Sbjct: 3   VIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 289 AALKSLNRSDIAGKRI 304
            A+K+ +   +  +  
Sbjct: 62  DAVKNADGYKLDKQHT 77

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 9/70 (12%)

Query: 154 TLFVRNINSNVED------SELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAART 204
            + V N+     D      + +  +F ++G I   +      K +G++ + Y     A  
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 205 AMRALQNKPL 214
           A++      L
Sbjct: 63  AVKNADGYKL 72

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            +  +    +LR+ F  +G V E+      E    R   FI F D ++ + A+ +++  D
Sbjct: 17  GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHD 75

Query: 299 IAGKRI 304
           I GK++
Sbjct: 76  IMGKKV 81

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 22/98 (22%), Positives = 44/98 (44%), Gaps = 14/98 (14%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVM 193
           G        S  +FV  I  N  ++ELR  F+++G +    T           + RGF  
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVV----TEVVMIYDAEKQRPRGFGF 56

Query: 194 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
           I++ D ++   A+  +    +  +K+++  + P+D+ S
Sbjct: 57  ITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKS 93

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFYDVRAAEAALKSLN 295
           T+ +     +V+ +++ +       V   I    H       F++F +    + ALK  N
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 296 RSDIAGKRIKLEPSRPG 312
           R  + G+ I++   + G
Sbjct: 71  REYMGGRYIEVFREKSG 87

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           G   S  +FV     ++ + ELR  F QYGD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPS 231
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 303
                ++ ++LR+ F  YG+V ++      R   F+ F D + A++         I G  
Sbjct: 12  RCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGIS 69

Query: 304 IKLEPSRP 311
           + +  + P
Sbjct: 70  VHISNAEP 77

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 45.9 bits (109), Expect = 3e-06
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFYD 283
               S +      + +  L    +  D+   F     ++  I   P  R      +EF  
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFAT 64

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 316
              A AA+   +++++  + ++L  +   G   
Sbjct: 65  HEDAVAAMA-KDKANMQHRYVELFLNSTAGTSG 96

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 44.3 bits (105), Expect = 5e-06
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 13/78 (16%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHK-------RHHK---FIEFYDVRAAEAALKS 293
           N+   ++ E +   F A   +  + + P            K   F+EF  V     A+ +
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A 71

Query: 294 LNRSDIAGKRIKLEPSRP 311
            +     G+ +K+   RP
Sbjct: 72  FDGIIFQGQSLKI--RRP 87

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 11/80 (13%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA----------CKHRGFVMISYYDIRA 201
           +R L+V NI   + +  +   F     +  L  A           + + F  + +  +  
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65

Query: 202 ARTAMRALQNKPLRRRKLDI 221
              AM A      + + L I
Sbjct: 66  TTQAM-AFDGIIFQGQSLKI 84

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 44.1 bits (105), Expect = 6e-06
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 283
           N S  + + G + V  L    S +DL+  F  +GEV +        T   R   FI F D
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 284 VRAAEAALKSLNRSDIAGKRI 304
             + E  L       + G+ I
Sbjct: 63  AASVEKVLDQKEH-RLDGRVI 82

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 13/72 (18%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISY 196
              E  +  +FV  ++ +    +L+  F ++G++      C         + RGF  I +
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV----VDCTIKMDPNTGRSRGFGFILF 60

Query: 197 YDIRAARTAMRA 208
            D  +    +  
Sbjct: 61  KDAASVEKVLDQ 72

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 245 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           L P    E +R+ FG +GEV+ I      +T  +R   FI F +    +  ++     ++
Sbjct: 7   LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNV 65

Query: 300 AGKRI 304
              + 
Sbjct: 66  GLSKC 70

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 41.3 bits (98), Expect = 5e-05
 Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 13/63 (20%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 205
           +FV  ++ +  + ++R  F  +G++     +          K RGF  I++ +    +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEV----ESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 206 MRA 208
           M  
Sbjct: 58  MEK 60

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 281
                        L+V  L    + +DL++ F  +GEV  +      +T H +   F+ F
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 282 YDVRAAEAALKSLNRSDIAGKRI 304
            +       +   +   I G+  
Sbjct: 65  TEYETQVKVMSQRH--MIDGRWC 85

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 11/95 (11%), Positives = 25/95 (26%), Gaps = 15/95 (15%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISY 196
                 +  L V  +     + +L+  F  +G++                  +GF  + +
Sbjct: 9   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEV----LMVQVKKDLKTGHSKGFGFVRF 64

Query: 197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
            +       M       +  R  D      K +  
Sbjct: 65  TEYETQVKVMSQRHM--IDGRWCDCKLPNSKQSQD 97

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 44.0 bits (104), Expect = 1e-05
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 2/79 (2%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRS 297
           + + NL    S +DL+ +               +       +EF        AL+ LN  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 298 DIAGKRIKLEPSRPGGARR 316
           +  G  I +E        R
Sbjct: 91  EFRGSVITVERDDNPPPIR 109

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.4 bits (92), Expect = 6e-04
 Identities = 11/98 (11%), Positives = 27/98 (27%), Gaps = 2/98 (2%)

Query: 126 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD--IRTLY 183
           G+   H+   +G                 + ++N+       +L+ L  +       +  
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61

Query: 184 TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI 221
                 G   + +        A+  L N   R   + +
Sbjct: 62  NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 9/91 (9%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK--------FIEFYDVRAA 287
           NQ  + +  L  + + E++   FG +  +   +E      +         F+ F     A
Sbjct: 22  NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYA 81

Query: 288 EAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
           + AL+  ++  +  + I+L  S     ++ L
Sbjct: 82  QNALR-KHKDLLGKRYIELFRSTAAEVQQVL 111

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.8 bits (104), Expect = 2e-05
 Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 12/103 (11%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 278
           ++P +    +      L +  L    + E LR  +  +G++ +        +   R   F
Sbjct: 14  TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKL------EPSRPGGAR 315
           + F  +   +AA+ +     I G+ ++       E S  G + 
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGSGPSS 115

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 14/98 (14%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVM 193
                 +   R LF+  ++    +  LR  +EQ+G +    T C         + RGF  
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKL----TDCVVMRDPASKRSRGFGF 73

Query: 194 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
           +++  +     AM A +   +  R ++   ++ ++   
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESG 110

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 12/80 (15%), Positives = 23/80 (28%), Gaps = 4/80 (5%)

Query: 151 PSRTLFVRNI-NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 209
             R + + +         +L  L E +G I              I       A+ A+   
Sbjct: 14  TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYY 72

Query: 210 QNKP--LRRRKLDIHFSIPK 227
              P  +  + + +H S   
Sbjct: 73  TTTPALVFGKPVRVHLSQKY 92

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 303
                ++ E+L+Q F  YGEV ++      R   F+ F D + A++         I G  
Sbjct: 18  RCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG--EDLIIKGIS 75

Query: 304 IKLEPSRPGGARRN 317
           + +  + P   + N
Sbjct: 76  VHISNAEPKHNKLN 89

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 202
           G H +  H S+ +FV     ++   EL+  F QYG++  ++     R F  +++ D + A
Sbjct: 3   GSHHHHHHGSK-VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDN 229
           ++     ++  ++   + I  + PK N
Sbjct: 62  QSLCG--EDLIIKGISVHISNAEPKHN 86

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 43.0 bits (101), Expect = 3e-05
 Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 8/93 (8%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHK----F 278
                  +      + +  L  S S ED++           V  +     +   +    F
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAF 65

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           +E       + ALK  +R  +  + I++  S  
Sbjct: 66  VELESEDDVKLALK-KDRESMGHRYIEVFKSHR 97

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 44.4 bits (104), Expect = 3e-05
 Identities = 8/75 (10%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDVRAAEAALKSL 294
           ++ +       + +D+++     G+V  I+      +  K   F+ F  + +A+  +++ 
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 295 NRSDIAGKRIKLEPS 309
            +       + +   
Sbjct: 171 GQK-YKETDLLILFK 184

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.1 bits (95), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 245 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           L  + + ED++  F  +G+V +      + T   R   F+ F      E   +  +  +I
Sbjct: 7   LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEI 65

Query: 300 AGKRI 304
             K +
Sbjct: 66  NNKMV 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.1 bits (95), Expect = 1e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 205
           +FV  ++ N    +++  FEQ+G +                +HRGF  +++         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV----DDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 206 MRA 208
              
Sbjct: 58  CEI 60

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 11/68 (16%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIR 200
           G   SR +FV  +  ++++ E+ A F ++G +   +       +    +G+  + + +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 201 AARTAMRA 208
           + +  + A
Sbjct: 64  SVQALIDA 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.7 bits (95), Expect = 2e-04
 Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 15/85 (17%)

Query: 242 VF--NLDPSVSNEDLRQIFGAYGEVKEI-------RETPHKRHHKFIEFYDVRAAEAALK 292
           VF   L P +  +++   F  +G +          +     + + F+ F +  + +A + 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 293 SLNRSD------IAGKRIKLEPSRP 311
           +    D      ++   IK +P + 
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKPVQI 95

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           + +  L    + E LR+ FG +GEVKE        T   R   F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 295 NRSDIAGKRIKLEPSR 310
           +R ++  K I  +P  
Sbjct: 62  SRHELDSKTI--DPKV 75

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.6 bits (91), Expect = 4e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 205
           +F+  ++       LR  F Q+G++      C         + RGF  +++ D       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV----KECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 206 MRA 208
           +  
Sbjct: 59  LAQ 61

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 10/92 (10%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 278
            +P+ +          + +  L    + E LR+ FG +GEVKE        T   R   F
Sbjct: 14  LVPRGSHMGSS--GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 310
           + F D    +  L   +R ++  K I  +P  
Sbjct: 72  VTFMDQAGVDKVLAQ-SRHELDSKTI--DPKV 100

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 11/89 (12%), Positives = 29/89 (32%), Gaps = 8/89 (8%)

Query: 228 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHK----FIE 280
               ++  +   +    L  S + ED+   F           I    ++   +     IE
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPS 309
               +  + AL+  +R  +  + +++   
Sbjct: 62  MESEQDVQKALE-KHRMYMGQRYVEVYEI 89

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------K 187
           G+   +G +  G      LFV  ++ +     LR+ F QYG++      C         +
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEV----VDCVIMKDKTTNQ 56

Query: 188 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 228
            RGF  + + D     T + + +   L  R +D     P+ 
Sbjct: 57  SRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRG 96

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 24/89 (26%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 281
               +      G L V  LD S + E LR  F  YGEV +      + T   R   F++F
Sbjct: 6   SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

Query: 282 YDVRAAEAALKSLNRSDIAGKRIKLEPSR 310
            D       L S     + G+ I  +P  
Sbjct: 66  KDPNCVGTVLAS-RPHTLDGRNI--DPKP 91

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 148 GEHPSRTLFVRNINSNV-----EDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 202
           G   S  L     N +V       ++  +LF  Y    T +   K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT-FQYFKSFKRVRINFSNPLSA 59

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKD 228
             A   L       +++ ++F+    
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLH 85

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 244 NLDPSVSNEDLRQIFGA-YGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN-RS 297
           +L P V +  L + F   Y   +  +    +T   + + F++F D    + AL       
Sbjct: 16  DLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAV 75

Query: 298 DIAGKRIKLEPSRPGGARR 316
            +  K ++L  + P  +R 
Sbjct: 76  GLGSKPVRLSVAIPKASRV 94

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 41.3 bits (96), Expect = 9e-04
 Identities = 28/140 (20%), Positives = 43/140 (30%), Gaps = 28/140 (20%)

Query: 216 RRKLDIHFSI-PKDNPSDKDLNQGTLVVFNLDPS--VSNEDLRQIFGAYGEVKEIRETPH 272
           +  L  H  I      +        LVV N      VS   L  +    G V  +   P+
Sbjct: 2   KHTLLRHEGIETVSYATQS------LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 55

Query: 273 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 332
           K  + F  +     ++ A  +LN           E     G +  L L   ++++  E R
Sbjct: 56  KP-YSFARYRTTEESKRAYVTLNGK---------EVVDDLGQKITLYLNFVEKVQWKELR 105

Query: 333 ILQHQVGSPITNSPPGNWVQ 352
                        PPG  V 
Sbjct: 106 ---------PQALPPGLMVV 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	818
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.98
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.95
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.94
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.94
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.92
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.81
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.78
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.78
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.77
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.77
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.74
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.74
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.7
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.65
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.63
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.62
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.62
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.6
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.59
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.57
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.57
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.56
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.55
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.55
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.55
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.54
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.54
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.54
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.54
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.54
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.54
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.54
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.54
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.54
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.53
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.53
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.53
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.53
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.53
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.53
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.52
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.52
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.52
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.52
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.52
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.52
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.52
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.52
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.52
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.51
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.51
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.51
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.51
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.51
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.51
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.51
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.51
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.51
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.51
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.51
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.51
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.51
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.51
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.51
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.51
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.51
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.51
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.51
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.51
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.51
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.51
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.51
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.5
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.5
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.5
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.5
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.5
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.5
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.5
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.5
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.5
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.5
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.5
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.5
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.5
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.5
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.5
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.49
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.49
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.49
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.49
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.49
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.49
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.49
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.49
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.49
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.49
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.49
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.49
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.49
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.49
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.49
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.49
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.48
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.48
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.48
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.48
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.48
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.48
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.48
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.48
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.48
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.48
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.48
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.48
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.48
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.48
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.48
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.48
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.48
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.48
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.48
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.48
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.48
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.48
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.47
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.47
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.47
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.47
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.47
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.47
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.47
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.47
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.47
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.47
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.47
2div_A	99	TRNA selenocysteine associated protein; structural	99.46
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.46
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.46
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.46
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.46
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.46
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.46
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.46
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.46
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.46
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.46
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.46
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.46
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.46
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.46
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.46
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.46
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.45
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.45
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.45
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.45
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.45
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.45
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.45
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.45
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.45
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.45
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.45
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.45
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.45
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.45
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.45
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.45
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.45
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.45
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.45
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.45
2div_A	99	TRNA selenocysteine associated protein; structural	99.45
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.45
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.45
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.45
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.45
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.45
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.44
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.44
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.44
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.44
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.44
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.44
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.44
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.44
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.44
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.44
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.44
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.44
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.44
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.44
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.44
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.44
1x5p_A	97	Negative elongation factor E; structure genomics,	99.44
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.44
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.44
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.44
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.44
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.44
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.44
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.44
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.43
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.43
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.43
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.43
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.43
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.43
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.43
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.43
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.43
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.43
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.43
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.42
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.42
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.42
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.42
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.42
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.42
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.42
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.42
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.42
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.42
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.41
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.41
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.41
1x5p_A	97	Negative elongation factor E; structure genomics,	99.41
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.41
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.41
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.41
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.41
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.41
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.4
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.4
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.4
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.4
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.4
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.4
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.4
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.4
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.39
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.39
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.39
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.39
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.39
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.39
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.39
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.39
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.39
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.39
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.38
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.38
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.38
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.38
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.38
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.37
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.37
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.37
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.37
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.37
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.37
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.37
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.37
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.37
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.36
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.36
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.36
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.35
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.35
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.35
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.35
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.35
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.34
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.34
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.34
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.33
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.33
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.33
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.33
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.32
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.32
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.32
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.32
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.99
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.31
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.31
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.31
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.31
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.98
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.31
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.31
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.31
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.3
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.3
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.3
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.3
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.29
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.29
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.29
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.29
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.28
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.28
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.28
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.27
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.27
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.27
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.25
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.24
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.24
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.22
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.21
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.21
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.21
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.21
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.2
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.2
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.2
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.19
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.18
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.15
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.14
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.07
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.05
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.02
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.98
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.98
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.97
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.94
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.91
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.9
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.86
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.79
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.7
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.64
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.58
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	98.46
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.44
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.38
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.3
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.28
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.18
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.03
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.96
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.57
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.54
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.52
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.97
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.49
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.4
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.59
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.45
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.33
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.2
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.11
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.08
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	94.07
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.19
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.58
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.69
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	85.82

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=2.6e-32  Score=290.84  Aligned_cols=237  Identities=16%  Similarity=0.231  Sum_probs=199.7

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEEEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYGE  149 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~~~e  149 (818)
                      .+.++|++||.++++.++.++|+.+|-+.+..    +.++|++||.|.+.+.|.    .+++..+.+....+..     .
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~Gi~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~-----~   92 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYELKYCFV----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL-----Q   92 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSCEEEEEE----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE-----C
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCEEEEE----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe-----c
Confidence            47899999999999999999999999223433    567899999999987654    2333444443333332     2


Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.++|||+|||.++++++|+++|+.||.|..+++     +++++|||||+|.+.++|++|++.|++..+.|+.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35689999999999999999999999999998873     5678999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCC-CHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCcc
Q 003463          225 IPKDNPSDKDLNQGTLVVFNLDPSV-SNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI  299 (818)
Q Consensus       225 ~pk~~~~~~~~~~~tL~V~NLp~~v-teedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i  299 (818)
                      .++.... ......+|||+|||.++ |+++|+++|++||.|..+++    ++.++|+|||+|.+.++|.+|+..|||..+
T Consensus       173 ~~~~~~~-~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  251 (284)
T 3smz_A          173 DAGQLTP-ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSL  251 (284)
T ss_dssp             CGGGCCT-TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCc-ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            8765432 33456799999999996 99999999999999999875    345689999999999999999999999999


Q ss_pred             CCceEEEEecCCCcccchhhh
Q 003463          300 AGKRIKLEPSRPGGARRNLML  320 (818)
Q Consensus       300 ~Gr~L~V~~a~~~~~r~~~~~  320 (818)
                      .|++|+|.|++++..++..+.
T Consensus       252 ~g~~l~v~~a~~~~~~~~~~~  272 (284)
T 3smz_A          252 GGSHLRVSFCAPGPPGRSMLA  272 (284)
T ss_dssp             TTEECEEEECCSSSCHHHHHH
T ss_pred             CCeEEEEEEecCCCcccchhh
Confidence            999999999999887665443

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.98  E-value=1.2e-31  Score=286.75  Aligned_cols=230  Identities=18%  Similarity=0.275  Sum_probs=189.2

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccc---cCccccCCCCccccCCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG---LLHYSVPNGAGTVAGEHPY  147 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~---~~~~~l~n~~~~~~g~~~~  147 (818)
                      .+.++|++||.++++.++.++|..+|.|   .|..+..  .++|++||.|.+.+.|..   +.+..+.+....+..    
T Consensus        41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~----  114 (292)
T 2ghp_A           41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSH----  114 (292)
T ss_dssp             -CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEE----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC--CCcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEE----
Confidence            5789999999999999999999999987   3444543  357999999999886553   333333333222222    


Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG-~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                        ...++|||+|||.++++++|+++|+.|| .|..|++    .++++|||||+|.+.++|++|++.|++..+.|+.|.|.
T Consensus       115 --~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  192 (292)
T 2ghp_A          115 --LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK  192 (292)
T ss_dssp             --CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             --CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence              2578999999999999999999999999 9999984    34689999999999999999999999999999999999


Q ss_pred             ccCCCCCCCC---CCCCccceeeecCCCC-CCHHHHHHHhhccCCeEEEEec------CCCCceEEEEEcCHHHHHHHHH
Q 003463          223 FSIPKDNPSD---KDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALK  292 (818)
Q Consensus       223 ~a~pk~~~~~---~~~~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~------g~srG~aFVeF~d~e~A~~Ai~  292 (818)
                      ++.++.....   ......+|||+|||.. +|+++|+++|++||.|..|++.      +.++|||||+|.+.++|.+|+ 
T Consensus       193 ~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-  271 (292)
T 2ghp_A          193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-  271 (292)
T ss_dssp             ECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-
T ss_pred             ECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-
Confidence            9987654332   2334579999999999 9999999999999999999863      667899999999999999999 


Q ss_pred             HcCCCccCCceEEEEecCCC
Q 003463          293 SLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       293 ~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      .|||..|.|++|+|.|++++
T Consensus       272 ~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          272 QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             GGTTEEETTEEEEEEECCCC
T ss_pred             HhcCCEECCcEEEEEEecCC
Confidence            99999999999999999876

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=2e-29  Score=258.59  Aligned_cols=166  Identities=19%  Similarity=0.349  Sum_probs=146.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..|.++|||+|||.++||++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            357899999999999999999999999999999984     577899999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe---cCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       224 a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~---~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      +......  ......+|||+|||+.+|+++|+++|++||.|+.|++   .+.++|||||+|.+.++|.+|++.|||..|.
T Consensus        92 ~~~~~~~--~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~  169 (213)
T 4f02_A           92 SQRDPSL--RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN  169 (213)
T ss_dssp             CCCCTHH--HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             ccccccc--cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            8654321  2224568999999999999999999999999999976   3446899999999999999999999999999


Q ss_pred             CceEEEEecCCCcccc
Q 003463          301 GKRIKLEPSRPGGARR  316 (818)
Q Consensus       301 Gr~L~V~~a~~~~~r~  316 (818)
                      |++|+|++++++.++.
T Consensus       170 g~~i~V~~a~~~~~~~  185 (213)
T 4f02_A          170 DRKVFVGRFKSRKERE  185 (213)
T ss_dssp             TEECEEEECCCHHHHH
T ss_pred             CEEEEEEEcCCCcccc
Confidence            9999999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=3e-28  Score=236.68  Aligned_cols=157  Identities=20%  Similarity=0.361  Sum_probs=142.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      |+|||+|||.++|+++|+++|++||+|..|++    .++++|||||+|.+.++|++|++.|++..+.|+.|.|.++.+..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            68999999999999999999999999999984    35678999999999999999999999999999999999987665


Q ss_pred             CCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce
Q 003463          229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  303 (818)
Q Consensus       229 ~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~  303 (818)
                      ..  ......+|||+|||..+|+++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.|++
T Consensus        81 ~~--~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  158 (166)
T 3md3_A           81 QS--SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP  158 (166)
T ss_dssp             CC--CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CC--CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Confidence            32  3345679999999999999999999999999999876     3556889999999999999999999999999999


Q ss_pred             EEEEecCC
Q 003463          304 IKLEPSRP  311 (818)
Q Consensus       304 L~V~~a~~  311 (818)
                      |+|.||++
T Consensus       159 i~v~~a~~  166 (166)
T 3md3_A          159 LRINWAAK  166 (166)
T ss_dssp             CEEEESCC
T ss_pred             EEEEecCC
Confidence            99999864

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.95  E-value=7.4e-28  Score=235.04  Aligned_cols=155  Identities=23%  Similarity=0.429  Sum_probs=141.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ++++|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            5789999999999999999999999999999983     56688999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      ++..    .....+|+|+|||..+++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
T Consensus        82 ~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  157 (168)
T 1b7f_A           82 PGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE  157 (168)
T ss_dssp             CCSS----TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEec
Confidence            7543    335679999999999999999999999999999875     4455799999999999999999999999998


Q ss_pred             C--ceEEEEec
Q 003463          301 G--KRIKLEPS  309 (818)
Q Consensus       301 G--r~L~V~~a  309 (818)
                      |  ++|+|+||
T Consensus       158 g~~~~l~V~~A  168 (168)
T 1b7f_A          158 GGSQPLSVRLA  168 (168)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCCeEEEEEeC
Confidence            8  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.95  E-value=9.1e-28  Score=233.52  Aligned_cols=155  Identities=25%  Similarity=0.441  Sum_probs=140.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ++++|||+|||.++++++|+++|+.||.|..+++     +++++|||||+|.+.++|++|++.|++..+.|++|+|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            4689999999999999999999999999999874     56788999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      +...    .....+|||+|||..+++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
T Consensus        81 ~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  156 (167)
T 1fxl_A           81 PSSA----SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS  156 (167)
T ss_dssp             CCCG----GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccC
Confidence            6542    335578999999999999999999999999999876     3446899999999999999999999999999


Q ss_pred             Cce--EEEEec
Q 003463          301 GKR--IKLEPS  309 (818)
Q Consensus       301 Gr~--L~V~~a  309 (818)
                      |+.  |+|+||
T Consensus       157 g~~~~i~v~~A  167 (167)
T 1fxl_A          157 GATEPITVKFA  167 (167)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCccceEEEeC
Confidence            964  888886

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.95  E-value=3.2e-27  Score=244.87  Aligned_cols=164  Identities=26%  Similarity=0.355  Sum_probs=147.0

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          149 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       149 e~~srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ..++++|||+|||. ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|++..+.|+.|.|.++.++
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            35689999999999 99999999999999999999976666899999999999999999999999999999999998754


Q ss_pred             CCCCCC-------------------------------CCCccceeeecCCCCCCHHHHHHHhhccC-CeEEEEecCCCCc
Q 003463          228 DNPSDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRH  275 (818)
Q Consensus       228 ~~~~~~-------------------------------~~~~~tL~V~NLp~~vteedL~~lFs~fG-~I~~vr~~g~srG  275 (818)
                      .....+                               .....+|||+|||..+++++|+++|++|| .|..|++....+|
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g  190 (229)
T 2adc_A          111 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK  190 (229)
T ss_dssp             CCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTT
T ss_pred             cccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCc
Confidence            211100                               11246899999999999999999999999 9999999777789


Q ss_pred             eEEEEEcCHHHHHHHHHHcCCCccC-CceEEEEecCCC
Q 003463          276 HKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG  312 (818)
Q Consensus       276 ~aFVeF~d~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~~~  312 (818)
                      +|||+|.+.++|.+|++.|||..+. |++|+|.|++++
T Consensus       191 ~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999999999999999999999 999999999874

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.95  E-value=1.4e-27  Score=242.76  Aligned_cols=163  Identities=20%  Similarity=0.380  Sum_probs=143.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +.++|||+|||.++|+++|+++|+.||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4689999999999999999999999999999985     56789999999999999999999999999999999998876


Q ss_pred             CCCCCCC-------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHH
Q 003463          226 PKDNPSD-------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       226 pk~~~~~-------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~  293 (818)
                      .......       ......+|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence            5432110       1234469999999999999999999999999999976     345689999999999999999999


Q ss_pred             cCCCccCCceEEEEecCCCc
Q 003463          294 LNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       294 LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      |||..|.|+.|+|.|++++.
T Consensus       187 l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          187 MNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HTTCBCSSSBCEEEECSSCS
T ss_pred             ccCCEeCCcEEEEEEecCCC
Confidence            99999999999999998764

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.95  E-value=5.9e-28  Score=238.17  Aligned_cols=161  Identities=19%  Similarity=0.279  Sum_probs=144.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE----EeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v----~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..+    ..+++++|||||+|.+.++|++|++ |++..+.|++|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            4568999999999999999999999999864331    1357789999999999999999995 9999999999999999


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          225 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       225 ~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                      .++...  ......+|||+|||..+|+++|+++|++||.|..+..++.++|+|||+|.+.++|.+|++.|||..+.|+.|
T Consensus        89 ~~~~~~--~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  166 (175)
T 1fje_B           89 KGRDSK--KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV  166 (175)
T ss_dssp             CCSSCS--TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEE
T ss_pred             CCcccc--ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            876532  334567999999999999999999999999999986677889999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 003463          305 KLEPSRPG  312 (818)
Q Consensus       305 ~V~~a~~~  312 (818)
                      +|+|++++
T Consensus       167 ~v~~a~~k  174 (175)
T 1fje_B          167 SLYYTGEK  174 (175)
T ss_dssp             EEEECSSC
T ss_pred             EEEecCCC
Confidence            99999875

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.95  E-value=3.2e-27  Score=236.56  Aligned_cols=166  Identities=19%  Similarity=0.374  Sum_probs=139.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++|+++|+++|+.||.|..|++     +++++|||||+|.+.++|++|++. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            4456799999999999999999999999999999874     466899999999999999999985 8999999999999


Q ss_pred             ccCCCCCCCC--CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcC
Q 003463          223 FSIPKDNPSD--KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       223 ~a~pk~~~~~--~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      ++.++.....  ......+|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|+.. +
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~  166 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K  166 (196)
T ss_dssp             ECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S
T ss_pred             cccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C
Confidence            9876543221  2234579999999999999999999999999999976     455689999999999999999986 8


Q ss_pred             CCccCCceEEEEecCCCccc
Q 003463          296 RSDIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       296 G~~i~Gr~L~V~~a~~~~~r  315 (818)
                      |..+.|+.|+|.++.++...
T Consensus       167 ~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          167 YHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             CCEETTEECEEEECC-----
T ss_pred             CcEECCEEEEEEecCChhHh
Confidence            99999999999999987654

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.95  E-value=6.4e-27  Score=248.94  Aligned_cols=162  Identities=23%  Similarity=0.453  Sum_probs=145.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr----~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ..++++|||+|||.++++++|+    ++|++||.|..|++  +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            4678999999999999999977    89999999999985  67889999999999999999999999999999999999


Q ss_pred             ccCCCCCCC-----------------------------------------------------------------------
Q 003463          223 FSIPKDNPS-----------------------------------------------------------------------  231 (818)
Q Consensus       223 ~a~pk~~~~-----------------------------------------------------------------------  231 (818)
                      ++..+....                                                                       
T Consensus        86 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  165 (282)
T 3pgw_A           86 YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMP  165 (282)
T ss_pred             EeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCC
Confidence            986544200                                                                       


Q ss_pred             ------------------------------------CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCc
Q 003463          232 ------------------------------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH  275 (818)
Q Consensus       232 ------------------------------------~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG  275 (818)
                                                          .......+|||+|||..+++++|+++|++||.|++|++....+|
T Consensus       166 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g  245 (282)
T 3pgw_A          166 PPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD  245 (282)
T ss_pred             CCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCc
Confidence                                                01123467999999999999999999999999999998776679


Q ss_pred             eEEEEEcCHHHHHHHHHHcCCCccC-CceEEEEecC
Q 003463          276 HKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSR  310 (818)
Q Consensus       276 ~aFVeF~d~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~  310 (818)
                      +|||+|.+.++|.+|++.|||..+. |+.|+|+|++
T Consensus       246 ~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          246 IAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9999999999999999999999999 9999999986

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.95  E-value=6.2e-27  Score=249.28  Aligned_cols=178  Identities=19%  Similarity=0.317  Sum_probs=162.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      .++++|||+|||.++|+++|+++|+.|| |..+.+ ++++|||||+|.+.++|++|++.|++..+.|++|.|.++.    
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~----   93 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP----   93 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC----
Confidence            3578999999999999999999999999 999987 7789999999999999999999999999999999999864    


Q ss_pred             CCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       230 ~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                            ...+|||+|||.++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|+..|+|..+.|+.|
T Consensus        94 ------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           94 ------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             ------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence                  2358999999999999999999999999999865     45568999999999999999999999999999999


Q ss_pred             EEEecCCCcc-------cchhhhccchhc-cHHHHHHHHhhcC
Q 003463          305 KLEPSRPGGA-------RRNLMLQLNQEL-EQDESRILQHQVG  339 (818)
Q Consensus       305 ~V~~a~~~~~-------r~~~~~ql~~~~-~~~~l~~~f~~~G  339 (818)
                      +|.++.++..       +..++.++...+ ++++++.+|.+||
T Consensus       168 ~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G  210 (284)
T 3smz_A          168 YVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVH  210 (284)
T ss_dssp             EEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSS
T ss_pred             EEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCC
Confidence            9999987652       346888999996 8999999999887

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.95  E-value=3.7e-27  Score=237.62  Aligned_cols=162  Identities=26%  Similarity=0.363  Sum_probs=145.4

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          151 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       151 ~srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      .+++|||+|||. ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|++..+.|+.|.|.++.++..
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~   81 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   81 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCc
Confidence            368999999999 9999999999999999999997666689999999999999999999999999999999999875421


Q ss_pred             CCCC-------------------------------CCCccceeeecCCCCCCHHHHHHHhhccC-CeEEEEecCCCCceE
Q 003463          230 PSDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHK  277 (818)
Q Consensus       230 ~~~~-------------------------------~~~~~tL~V~NLp~~vteedL~~lFs~fG-~I~~vr~~g~srG~a  277 (818)
                      ...+                               .....+|||+|||..+++++|+++|++|| .|..+++....+|+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~a  161 (198)
T 1qm9_A           82 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA  161 (198)
T ss_dssp             CCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCE
T ss_pred             CCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEE
Confidence            1110                               11256899999999999999999999999 999999977779999


Q ss_pred             EEEEcCHHHHHHHHHHcCCCccC-CceEEEEecCCC
Q 003463          278 FIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG  312 (818)
Q Consensus       278 FVeF~d~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~~~  312 (818)
                      ||+|.+.++|.+|+..|||..+. |++|+|.|++++
T Consensus       162 fV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          162 LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999999999999999999999 999999999874

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.95  E-value=4.5e-27  Score=230.64  Aligned_cols=153  Identities=16%  Similarity=0.345  Sum_probs=139.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~f----G-------~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      ++++|||+|||.++|+++|+++|++|    |       .|..+++ ++++|||||+|.+.++|++|+ .+++..+.|++|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~-~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i   80 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe-cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCcee
Confidence            57899999999999999999999999    7       7888865 567999999999999999999 799999999999


Q ss_pred             cccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHc
Q 003463          220 DIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL  294 (818)
Q Consensus       220 ~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~L  294 (818)
                      +|.++.+....    ....+|||+|||..+|+++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|
T Consensus        81 ~v~~~~~~~~~----~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           81 KIRRPHDYQPL----PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             EEECCSSCCCC----TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             eecCCcccCCC----CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            99987654322    24678999999999999999999999999999976     4556899999999999999999999


Q ss_pred             CCCccCCceEEEEec
Q 003463          295 NRSDIAGKRIKLEPS  309 (818)
Q Consensus       295 nG~~i~Gr~L~V~~a  309 (818)
                      ||..+.|++|+|++|
T Consensus       157 ~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTCEETTEECEEEEC
T ss_pred             CCCEECCeEEEEEeC
Confidence            999999999999997

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.95  E-value=2e-27  Score=231.96  Aligned_cols=155  Identities=20%  Similarity=0.432  Sum_probs=139.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ++++|||+|||.++|+++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            5789999999999999999999999999999984     567899999999999999999994  678999999999886


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      ++.    ......+|||+|||.++++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++ ++|..+.
T Consensus        80 ~~~----~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~  154 (167)
T 2cjk_A           80 PRD----EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFK  154 (167)
T ss_dssp             CHH----HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSS
T ss_pred             chh----hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeC
Confidence            543    2234568999999999999999999999999999975     45678999999999999999998 8999999


Q ss_pred             CceEEEEecCCC
Q 003463          301 GKRIKLEPSRPG  312 (818)
Q Consensus       301 Gr~L~V~~a~~~  312 (818)
                      |++|+|.+++++
T Consensus       155 g~~i~V~~a~pk  166 (167)
T 2cjk_A          155 DRKIEIKRAEPR  166 (167)
T ss_dssp             SSCEEEEECCCC
T ss_pred             CeEEEEeecCCC
Confidence            999999999886

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.94  E-value=1.1e-26  Score=238.04  Aligned_cols=159  Identities=19%  Similarity=0.229  Sum_probs=137.4

Q ss_pred             CCcEEEEcCCC-CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          151 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       151 ~srtLfV~NLP-~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      ++++|||+||| .++++++|+++|++||.|.+|++....+|||||+|.+.++|++|++.|+|..+.|++|+|.++..+..
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~   82 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI   82 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCcc
Confidence            57899999999 89999999999999999999998777799999999999999999999999999999999999864321


Q ss_pred             CCC------------C---------------------CCCccceeeecCCCCCCHHHHHHHhhccCCe--EEEEecC---
Q 003463          230 PSD------------K---------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEIRETP---  271 (818)
Q Consensus       230 ~~~------------~---------------------~~~~~tL~V~NLp~~vteedL~~lFs~fG~I--~~vr~~g---  271 (818)
                      ...            +                     .....+|||+|||+++|+++|+++|++||.|  .++++..   
T Consensus        83 ~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~  162 (205)
T 3tyt_A           83 MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKS  162 (205)
T ss_dssp             CCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCS
T ss_pred             CCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCC
Confidence            000            0                     0123479999999999999999999999999  8887643   


Q ss_pred             CCCceEEEEEcCHHHHHHHHHHcCCCccCCc----eEEEEec
Q 003463          272 HKRHHKFIEFYDVRAAEAALKSLNRSDIAGK----RIKLEPS  309 (818)
Q Consensus       272 ~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr----~L~V~~a  309 (818)
                      .++|+|||+|.+.++|.+||..|||.+|.|+    ++.|+++
T Consensus       163 ~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          163 ERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            3468999999999999999999999999985    5776664

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.94  E-value=1.1e-26  Score=227.77  Aligned_cols=157  Identities=20%  Similarity=0.405  Sum_probs=136.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CC--CcccEEEEEEccHHHHHHHHHHhcCcccc---ccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----AC--KHRGFVMISYYDIRAARTAMRALQNKPLR---RRKLD  220 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~--ksrG~AFV~F~d~e~A~~Al~~Lng~~l~---gr~L~  220 (818)
                      ++++|||+|||.++|+++|+++|++||+|..|++     ++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            4689999999999999999999999999999874     22  78999999999999999999999998876   56777


Q ss_pred             ccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCC
Q 003463          221 IHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  296 (818)
Q Consensus       221 V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG  296 (818)
                      +.++.+...   ......+|||+|||..+|+++|+++|++||.|..+++    ++.++|||||+|.+.++|.+|++.|||
T Consensus        82 ~~~~~~~~~---~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           82 MKPADSEKN---NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGCC---SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Ecccccccc---ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            777655432   2345679999999999999999999999999999976    344688999999999999999999999


Q ss_pred             CccC---CceEEEEecC
Q 003463          297 SDIA---GKRIKLEPSR  310 (818)
Q Consensus       297 ~~i~---Gr~L~V~~a~  310 (818)
                      ..+.   |++|+|.||.
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            8776   4999999974

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.94  E-value=9.8e-27  Score=233.41  Aligned_cols=162  Identities=16%  Similarity=0.324  Sum_probs=142.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~f----G-------~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      .+++|||+|||.++|+++|+++|++|    |       .|..+.+ ++++|||||+|.+.++|++|+ .|++..+.|+.|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i   80 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceE
Confidence            57999999999999999999999999    6       7777765 678999999999999999999 799999999999


Q ss_pred             cccccCCCCCCCC----------------CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEE
Q 003463          220 DIHFSIPKDNPSD----------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKF  278 (818)
Q Consensus       220 ~V~~a~pk~~~~~----------------~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aF  278 (818)
                      +|.++.+......                ......+|||+|||..+++++|+++|++||.|..|++     ++.++||||
T Consensus        81 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~af  160 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF  160 (198)
T ss_dssp             EEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEE
T ss_pred             EEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEE
Confidence            9999866432110                1134579999999999999999999999999999976     445589999


Q ss_pred             EEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       279 VeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      |+|.+.++|.+|++.|||..+.|+.|+|++++++..
T Consensus       161 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999998764

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.94  E-value=3.2e-26  Score=244.75  Aligned_cols=181  Identities=20%  Similarity=0.270  Sum_probs=156.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ....+.++|||+|||.++|+++|+++|+.||+|..|++.   ..++|||||+|.+.++|++|++ +++..+.|+.|.|.+
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH  114 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEE
Confidence            345678999999999999999999999999999999842   2358999999999999999996 899999999999998


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccC-CeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       224 a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG-~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      +.           ..+|||+|||..+++++|+++|++|| .|..|++.    +.++|||||+|.+.++|.+|+..|+|..
T Consensus       115 ~~-----------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~  183 (292)
T 2ghp_A          115 LT-----------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK  183 (292)
T ss_dssp             CC-----------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CC-----------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            62           56899999999999999999999999 99999763    3568999999999999999999999999


Q ss_pred             cCCceEEEEecCCCcc-----------cchhhhccchh-ccHHHHHHHHhhcC
Q 003463          299 IAGKRIKLEPSRPGGA-----------RRNLMLQLNQE-LEQDESRILQHQVG  339 (818)
Q Consensus       299 i~Gr~L~V~~a~~~~~-----------r~~~~~ql~~~-~~~~~l~~~f~~~G  339 (818)
                      +.|+.|+|.++.+...           +..++.++... +++++++.+|.+||
T Consensus       184 ~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G  236 (292)
T 2ghp_A          184 IEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFG  236 (292)
T ss_dssp             ETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGS
T ss_pred             eCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccC
Confidence            9999999999876543           34578889999 99999999999998

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.92  E-value=8.8e-25  Score=231.10  Aligned_cols=157  Identities=27%  Similarity=0.411  Sum_probs=141.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|||+|||.++|+++|+++|+.||.|..|.+ .+++|||||+|.+.++|++|++.|++..+.|+.|.|.++.+  
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i-~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~--   95 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH--   95 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc--
Confidence            345689999999999999999999999999999986 56799999999999999999999999999999999999864  


Q ss_pred             CCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCC-CccC---
Q 003463          229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR-SDIA---  300 (818)
Q Consensus       229 ~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG-~~i~---  300 (818)
                              ..+|||+|||..+|+++|+++|++||.|..|++    ++.++|||||+|.+.++|.+|+..||+ ..+.   
T Consensus        96 --------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~  167 (261)
T 3sde_A           96 --------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT  167 (261)
T ss_dssp             --------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSS
T ss_pred             --------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCC
Confidence                    358999999999999999999999999999875    456789999999999999999999954 4444   


Q ss_pred             CceEEEEecCCCcccc
Q 003463          301 GKRIKLEPSRPGGARR  316 (818)
Q Consensus       301 Gr~L~V~~a~~~~~r~  316 (818)
                      +++|.|.++.+.....
T Consensus       168 ~r~i~v~~~~~~~~~~  183 (261)
T 3sde_A          168 PRPVIVEPMEQFDDED  183 (261)
T ss_dssp             CCBCEEEECCCEESSS
T ss_pred             CceEEEeeccccCccC
Confidence            8999999998765443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.81  E-value=6e-20  Score=188.11  Aligned_cols=155  Identities=13%  Similarity=0.238  Sum_probs=126.5

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccc----cCccccCCCCccccCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHP  146 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~----~~~~~l~n~~~~~~g~~~  146 (818)
                      ++.+||++||.+++|.++.++|+.+|.|   .|..|..+++++||+||.|.+.+.|..    +....+.+...++.....
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            5789999999999999999999999987   577888899999999999999875542    222223333222222111


Q ss_pred             C---CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          147 Y---GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       147 ~---~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      .   .....++|||+|||.++|+++|+++|++||.|..|++   .+.++|||||+|.+.++|++|++.|+|..|.|++|.
T Consensus        95 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~  174 (213)
T 4f02_A           95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF  174 (213)
T ss_dssp             CTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            1   1224579999999999999999999999999999874   455799999999999999999999999999999999


Q ss_pred             ccccCCCC
Q 003463          221 IHFSIPKD  228 (818)
Q Consensus       221 V~~a~pk~  228 (818)
                      |.++.++.
T Consensus       175 V~~a~~~~  182 (213)
T 4f02_A          175 VGRFKSRK  182 (213)
T ss_dssp             EEECCCHH
T ss_pred             EEEcCCCc
Confidence            99998754

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.80  E-value=3.6e-19  Score=180.69  Aligned_cols=157  Identities=13%  Similarity=0.231  Sum_probs=127.4

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  146 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~  146 (818)
                      .+.++|++||.++++.++.++|+.+|.|   .+..+..++..+|++||.|.+.+.|.    .+.+..+.+....+.....
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            5789999999999999999999999987   46667778899999999999987654    2344444444444432222


Q ss_pred             C------------CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHh
Q 003463          147 Y------------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL  209 (818)
Q Consensus       147 ~------------~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~L  209 (818)
                      .            ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHc
Confidence            1            1235689999999999999999999999999999884     4577999999999999999999999


Q ss_pred             cCcccccccccccccCCCCCC
Q 003463          210 QNKPLRRRKLDIHFSIPKDNP  230 (818)
Q Consensus       210 ng~~l~gr~L~V~~a~pk~~~  230 (818)
                      ++..|.|+.|.|.++.++..+
T Consensus       188 ~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          188 NLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             TTCBCSSSBCEEEECSSCSST
T ss_pred             cCCEeCCcEEEEEEecCCCCC
Confidence            999999999999999876543

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.79  E-value=4.5e-19  Score=172.64  Aligned_cols=150  Identities=21%  Similarity=0.326  Sum_probs=124.4

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCCC
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPY  147 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~~  147 (818)
                      +.++|++||.++++.++.++|+.+|.|   .+..+..++.++|++||.|.+.+.|.    .+.+..+.+....+....+.
T Consensus         4 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   83 (168)
T 1b7f_A            4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG   83 (168)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCC
Confidence            679999999999999999999999987   45566678899999999999987654    23444444444444333322


Q ss_pred             -CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccc--ccc
Q 003463          148 -GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKL  219 (818)
Q Consensus       148 -~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~L  219 (818)
                       ...+.++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|+|..+.|  ++|
T Consensus        84 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l  163 (168)
T 1b7f_A           84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL  163 (168)
T ss_dssp             SSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             cccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEE
Confidence             3356789999999999999999999999999999874     56678999999999999999999999999987  999


Q ss_pred             ccccc
Q 003463          220 DIHFS  224 (818)
Q Consensus       220 ~V~~a  224 (818)
                      +|.||
T Consensus       164 ~V~~A  168 (168)
T 1b7f_A          164 SVRLA  168 (168)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.79  E-value=5.5e-19  Score=176.59  Aligned_cols=156  Identities=17%  Similarity=0.274  Sum_probs=121.7

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccc---cCccccCCCCccccCC---
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG---LLHYSVPNGAGTVAGE---  144 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~---~~~~~l~n~~~~~~g~---  144 (818)
                      .+.++|++||.++++.++.++|..+|.|   .|..+..++.++||+||.|.+.+.|..   ..+..+.+....+...   
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~   92 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   92 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCc
Confidence            5789999999999999999999999987   577787889999999999999875542   2222233322222111   


Q ss_pred             ----CCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          145 ----HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       145 ----~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                          .+....+.++|||+|||.++|+++|+++|+.||.|..|.+     +++++|||||+|.+.++|++|++. ++..|.
T Consensus        93 ~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~  171 (196)
T 1l3k_A           93 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVN  171 (196)
T ss_dssp             ----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEET
T ss_pred             ccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEEC
Confidence                1122335689999999999999999999999999999874     567899999999999999999996 799999


Q ss_pred             cccccccccCCCCCC
Q 003463          216 RRKLDIHFSIPKDNP  230 (818)
Q Consensus       216 gr~L~V~~a~pk~~~  230 (818)
                      |+.|.|.++.++...
T Consensus       172 G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          172 GHNCEVRKALSKQEM  186 (196)
T ss_dssp             TEECEEEECC-----
T ss_pred             CEEEEEEecCChhHh
Confidence            999999999887654

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.78  E-value=8.9e-19  Score=169.88  Aligned_cols=150  Identities=21%  Similarity=0.297  Sum_probs=123.2

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccc----cCccccCCCCccccCCCCC
Q 003463           75 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHPY  147 (818)
Q Consensus        75 ~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~----~~~~~l~n~~~~~~g~~~~  147 (818)
                      +.++|++||.++++.++.++|+.+|.|   .+..+..++.++|++||.|.+.+.|..    +.+..+.+....+....+.
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   82 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCC
Confidence            679999999999999999999999987   466777789999999999999876542    3444444444444333222


Q ss_pred             -CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccc--c
Q 003463          148 -GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK--L  219 (818)
Q Consensus       148 -~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~--L  219 (818)
                       ...+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.  |
T Consensus        83 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i  162 (167)
T 1fxl_A           83 SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI  162 (167)
T ss_dssp             CGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             cccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccce
Confidence             2345689999999999999999999999999999874     4667999999999999999999999999999975  6


Q ss_pred             ccccc
Q 003463          220 DIHFS  224 (818)
Q Consensus       220 ~V~~a  224 (818)
                      +|.||
T Consensus       163 ~v~~A  167 (167)
T 1fxl_A          163 TVKFA  167 (167)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            66664

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.78  E-value=5.8e-19  Score=171.04  Aligned_cols=127  Identities=19%  Similarity=0.244  Sum_probs=112.7

Q ss_pred             CCcccEEEEEEccHHHHHHHHHHh-cCcccccccccccccCCCC------------CCCCCCCCccceeeecCCCCCCHH
Q 003463          186 CKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIHFSIPKD------------NPSDKDLNQGTLVVFNLDPSVSNE  252 (818)
Q Consensus       186 ~ksrG~AFV~F~d~e~A~~Al~~L-ng~~l~gr~L~V~~a~pk~------------~~~~~~~~~~tL~V~NLp~~vtee  252 (818)
                      .+.+|+++|+|.+.++|++|++.+ ++..+.| .+.+.++..+.            .........++|||+|||+.+|++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            356899999999999999999999 9999999 99999876521            112223455799999999999999


Q ss_pred             HHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          253 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       253 dL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      +|+++|++||.|.+|++...++|||||+|.+.++|.+|+..|||..+.|++|+|++++++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            9999999999999999977789999999999999999999999999999999999998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.78  E-value=8.7e-19  Score=169.77  Aligned_cols=149  Identities=19%  Similarity=0.286  Sum_probs=121.7

Q ss_pred             ccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccC---CC
Q 003463           76 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAG---EH  145 (818)
Q Consensus        76 e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g---~~  145 (818)
                      .++|++||.++++.++.++|+.+|.|   .+..+. .+.++|++||.|.+.+.|.    .+.+..+.+....+..   ..
T Consensus         2 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             EEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999987   344444 5778999999999987554    3344444444333321   22


Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      .....+.++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|+|..+.|++|+
T Consensus        81 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  160 (166)
T 3md3_A           81 QSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR  160 (166)
T ss_dssp             CCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Confidence            234456789999999999999999999999999999874     467899999999999999999999999999999999


Q ss_pred             ccccC
Q 003463          221 IHFSI  225 (818)
Q Consensus       221 V~~a~  225 (818)
                      |.|+.
T Consensus       161 v~~a~  165 (166)
T 3md3_A          161 INWAA  165 (166)
T ss_dssp             EEESC
T ss_pred             EEecC
Confidence            99985

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.78  E-value=1.6e-19  Score=175.93  Aligned_cols=153  Identities=18%  Similarity=0.275  Sum_probs=122.7

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhccccCc--cccCCCCccccCCCCC-
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLLH--YSVPNGAGTVAGEHPY-  147 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~~~~~--~~l~n~~~~~~g~~~~-  147 (818)
                      .+.++|++||.++++.++.++|+.+|.|   .+..+..++.++||+||.|.+.+.|.....  ..+.+....+....+. 
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~   82 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRD   82 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchh
Confidence            3679999999999999999999999987   456666789999999999998875542211  1122222222211111 


Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++ +++..+.|++|+|.
T Consensus        83 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~  161 (167)
T 2cjk_A           83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIK  161 (167)
T ss_dssp             HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEE
T ss_pred             hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEe
Confidence            1234679999999999999999999999999999983     46789999999999999999998 89999999999999


Q ss_pred             ccCCC
Q 003463          223 FSIPK  227 (818)
Q Consensus       223 ~a~pk  227 (818)
                      ++.|+
T Consensus       162 ~a~pk  166 (167)
T 2cjk_A          162 RAEPR  166 (167)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99875

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.78  E-value=1.1e-18  Score=170.87  Aligned_cols=152  Identities=15%  Similarity=0.265  Sum_probs=120.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCC--CcccEEEEEecChhhcc----ccCccccCCC---Cccc
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQES--LSMSMSKISISDSASGN----GLLHYSVPNG---AGTV  141 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~--~skG~a~v~f~~~~~a~----~~~~~~l~n~---~~~~  141 (818)
                      .+.++|++||.++++.++.++|..+|.|   .|..+..++  .++||+||.|.+.+.|.    .+.+..+..+   ...+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            3679999999999999999999999987   466676665  89999999999987554    2333233221   1111


Q ss_pred             --cCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          142 --AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       142 --~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                        .........+.++|||+|||.++|+++|+++|++||.|..+++    .++++|||||+|.+.++|++|++.|+|..+.
T Consensus        83 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  162 (175)
T 3nmr_A           83 KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM  162 (175)
T ss_dssp             EECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCC
T ss_pred             ccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCccc
Confidence              1111223346789999999999999999999999999999874    4567999999999999999999999998776


Q ss_pred             ---cccccccccC
Q 003463          216 ---RRKLDIHFSI  225 (818)
Q Consensus       216 ---gr~L~V~~a~  225 (818)
                         +++|.|.|+.
T Consensus       163 ~g~~~~l~V~~ad  175 (175)
T 3nmr_A          163 EGCSSPMVVKFAD  175 (175)
T ss_dssp             TTCSSCCEEEECC
T ss_pred             CCCCCCeEEEecC
Confidence               4999999873

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.77  E-value=3e-18  Score=167.05  Aligned_cols=130  Identities=21%  Similarity=0.281  Sum_probs=102.9

Q ss_pred             CCCcccEEEEEEccHHHHHHHHHHhcCcccc-------cccccccccCCCC--CCCCCCCCccceeeecCCCCCCHHHHH
Q 003463          185 ACKHRGFVMISYYDIRAARTAMRALQNKPLR-------RRKLDIHFSIPKD--NPSDKDLNQGTLVVFNLDPSVSNEDLR  255 (818)
Q Consensus       185 ~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~-------gr~L~V~~a~pk~--~~~~~~~~~~tL~V~NLp~~vteedL~  255 (818)
                      ..+++|||||+|.+.++|++|++.+++....       +............  ..........+|||+|||+++|+++|+
T Consensus         9 ~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~   88 (158)
T 2kn4_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLR   88 (158)
T ss_dssp             CSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHH
T ss_pred             CccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHH
Confidence            4468999999999999999999887753322       2222222111111  111223446799999999999999999


Q ss_pred             HHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          256 QIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       256 ~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++++..
T Consensus        89 ~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           89 RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             HHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999976     466799999999999999999999999999999999999987653

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.77  E-value=1.7e-19  Score=177.55  Aligned_cols=154  Identities=14%  Similarity=0.137  Sum_probs=126.9

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEE--EeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCccccCCCC--
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGME--LEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVAGEHP--  146 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i~--V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~~~~g~~~--  146 (818)
                      ...++|++||.++++.++.++|..+|.+.  +..+..++.++||+||.|.+.+.|.   .+++..+.+....+....+  
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~   92 (175)
T 1fje_B           13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRD   92 (175)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSS
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCcc
Confidence            47899999999999999999999988652  3455667889999999999887554   3444444444333332222  


Q ss_pred             -CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          147 -YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       147 -~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                       ....+.++|||+|||.++++++|+++|++||.|..+..+++++|||||+|.+.++|++|++.|+|..|.|+.|.|.|+.
T Consensus        93 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           93 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             CSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             ccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence             2334678999999999999999999999999999885577899999999999999999999999999999999999998


Q ss_pred             CC
Q 003463          226 PK  227 (818)
Q Consensus       226 pk  227 (818)
                      ++
T Consensus       173 ~k  174 (175)
T 1fje_B          173 EK  174 (175)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.74  E-value=5.2e-18  Score=165.99  Aligned_cols=148  Identities=14%  Similarity=0.270  Sum_probs=118.4

Q ss_pred             ccccccccCCCCCChHHHHHhhcCC----C-------cEEEeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCc
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSG----G-------GMELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAG  139 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~----G-------~i~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~  139 (818)
                      .+.++|++||.++++.++.++|+.+    |       .|   .+......+|++||.|.+.+.|.   .+++..+.+...
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v---~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i   80 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV---LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSE---EEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCce---eeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCcee
Confidence            3789999999999999999999999    4       33   12234566899999999887554   333333433333


Q ss_pred             cccCCCCC-CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcc
Q 003463          140 TVAGEHPY-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKP  213 (818)
Q Consensus       140 ~~~g~~~~-~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~  213 (818)
                      .+...... .....++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|+|..
T Consensus        81 ~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (172)
T 2g4b_A           81 KIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ  160 (172)
T ss_dssp             EEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCE
T ss_pred             eecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCE
Confidence            33322222 2234689999999999999999999999999999884     56779999999999999999999999999


Q ss_pred             ccccccccccc
Q 003463          214 LRRRKLDIHFS  224 (818)
Q Consensus       214 l~gr~L~V~~a  224 (818)
                      +.|++|.|.+|
T Consensus       161 ~~g~~l~V~~A  171 (172)
T 2g4b_A          161 LGDKKLLVQRA  171 (172)
T ss_dssp             ETTEECEEEEC
T ss_pred             ECCeEEEEEeC
Confidence            99999999986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.74  E-value=6.9e-18  Score=168.87  Aligned_cols=156  Identities=12%  Similarity=0.210  Sum_probs=120.9

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---E-----EeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCcccc
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---E-----LEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVA  142 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~-----V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~~~~  142 (818)
                      .+.++|++||.++++.++.++|+.+|.+   .     ...+...+.++||+||.|.+.+.|.   .+++..+.+....+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~   83 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   83 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEE
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEe
Confidence            4789999999999999999999999522   0     1123334677899999999877554   233333333222221


Q ss_pred             CCCC---------------------CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEE
Q 003463          143 GEHP---------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISY  196 (818)
Q Consensus       143 g~~~---------------------~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F  196 (818)
                      ....                     ....+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f  163 (198)
T 2yh0_A           84 RPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY  163 (198)
T ss_dssp             CCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEE
T ss_pred             CCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEE
Confidence            1111                     11246789999999999999999999999999999884     566799999999


Q ss_pred             ccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       197 ~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      .+.++|++|++.|+|..|.|+.|.|.++.++..
T Consensus       164 ~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          164 VDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             SSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999987653

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.73  E-value=7.1e-18  Score=156.49  Aligned_cols=103  Identities=16%  Similarity=0.317  Sum_probs=72.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      .+++|||+|||+++|+++|+++|++||.|.+|++   .+.++|||||+|.+.++|++|++.|++..|.|++|+|.++.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            3678999999999999999999999999999874   4557899999999999999999999999999999999999876


Q ss_pred             CCCCC----CCCCccceeeecCCCCCCHHH
Q 003463          228 DNPSD----KDLNQGTLVVFNLDPSVSNED  253 (818)
Q Consensus       228 ~~~~~----~~~~~~tL~V~NLp~~vteed  253 (818)
                      .....    ......+|||+|||+++|++.
T Consensus        84 ~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccccccccCCCCceEeCCCCCCccccc
Confidence            54322    122335799999999999864

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.72  E-value=2.6e-17  Score=174.72  Aligned_cols=152  Identities=14%  Similarity=0.161  Sum_probs=119.2

Q ss_pred             ccccccccCCCCCChHHHH----HhhcCCCcEEEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDY----DIFGSGGGMELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH  145 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~----diF~~~G~i~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~  145 (818)
                      .+.+||++||.++++.++.    ++|..+|.|.-..-..++..+||+||.|.+.+.|.    .+++..+.+...++....
T Consensus         9 ~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   88 (282)
T 3pgw_A            9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   88 (282)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEec
Confidence            4789999999999999955    89999999843232337889999999999877554    233333332211111000


Q ss_pred             --------------------------------------------------------------------------------
Q 003463          146 --------------------------------------------------------------------------------  145 (818)
Q Consensus       146 --------------------------------------------------------------------------------  145 (818)
                                                                                                      
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~  168 (282)
T 3pgw_A           89 TDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPG  168 (282)
T ss_pred             cCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCCCCC
Confidence                                                                                            


Q ss_pred             --------------------------------CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEE
Q 003463          146 --------------------------------PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVM  193 (818)
Q Consensus       146 --------------------------------~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AF  193 (818)
                                                      .....++++|||+|||.++++++|+++|++||.|..|++....+||||
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~af  248 (282)
T 3pgw_A          169 MIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAF  248 (282)
T ss_pred             CCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEE
Confidence                                            012235689999999999999999999999999999987655579999


Q ss_pred             EEEccHHHHHHHHHHhcCcccc-cccccccccC
Q 003463          194 ISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  225 (818)
Q Consensus       194 V~F~d~e~A~~Al~~Lng~~l~-gr~L~V~~a~  225 (818)
                      |+|.+.++|++|++.|+|..|. |+.|+|.|++
T Consensus       249 V~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          249 VEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9999999999999999999999 9999999975

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.72  E-value=3.6e-17  Score=169.27  Aligned_cols=149  Identities=19%  Similarity=0.225  Sum_probs=119.9

Q ss_pred             ccccccccCCC-CCChHHHHHhhcCCCcEE---EeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCC
Q 003463           74 MDDFDLRGLPS-SLEDLEDYDIFGSGGGME---LEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH  145 (818)
Q Consensus        74 ~~e~~V~~Lp~-s~~E~el~diF~~~G~i~---V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~  145 (818)
                      ...++|++||. ++++.++.++|+.+|.|.   |..+.     +||+||.|.+.+.|.    .+++..+.+....+....
T Consensus        34 ~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  108 (229)
T 2adc_A           34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            47899999999 999999999999999873   33332     789999999987554    234444433322221111


Q ss_pred             C------------------------------------CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEeCCCc
Q 003463          146 P------------------------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYTACKH  188 (818)
Q Consensus       146 ~------------------------------------~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG-~I~~v~~~~ks  188 (818)
                      .                                    ....++++|||+|||.++++++|+++|++|| .|..|++..+.
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~  188 (229)
T 2adc_A          109 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD  188 (229)
T ss_dssp             CCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSS
T ss_pred             CccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECC
Confidence            0                                    0123468999999999999999999999999 99999986667


Q ss_pred             ccEEEEEEccHHHHHHHHHHhcCcccc-cccccccccCCC
Q 003463          189 RGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSIPK  227 (818)
Q Consensus       189 rG~AFV~F~d~e~A~~Al~~Lng~~l~-gr~L~V~~a~pk  227 (818)
                      +|||||+|.+.++|++|++.|+|..+. |++|+|.|+.++
T Consensus       189 ~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          189 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999999999999999999999999 999999998763

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.70  E-value=3.2e-17  Score=164.77  Aligned_cols=150  Identities=19%  Similarity=0.220  Sum_probs=118.3

Q ss_pred             cccccccCCC-CCChHHHHHhhcCCCcE-EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCC--
Q 003463           75 DDFDLRGLPS-SLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP--  146 (818)
Q Consensus        75 ~e~~V~~Lp~-s~~E~el~diF~~~G~i-~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~--  146 (818)
                      +.++|++||. ++++.++.++|+.+|.| .|.+-..   .+|++||.|.+.+.|.    .+++..+.+....+.....  
T Consensus         4 ~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN---KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTT---CSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            6799999999 99999999999999987 2322211   1789999999877554    2333334333222211100  


Q ss_pred             ----------------------------------CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEeCCCcccE
Q 003463          147 ----------------------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYTACKHRGF  191 (818)
Q Consensus       147 ----------------------------------~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG-~I~~v~~~~ksrG~  191 (818)
                                                        ....++++|||+|||.++++++|+++|++|| .|..+++....+|+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~  160 (198)
T 1qm9_A           81 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM  160 (198)
T ss_dssp             CCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSC
T ss_pred             cCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcE
Confidence                                              0123578999999999999999999999999 99999986667999


Q ss_pred             EEEEEccHHHHHHHHHHhcCcccc-cccccccccCCC
Q 003463          192 VMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSIPK  227 (818)
Q Consensus       192 AFV~F~d~e~A~~Al~~Lng~~l~-gr~L~V~~a~pk  227 (818)
                      |||+|.+.++|++|++.|+|..+. |++|+|.|+.++
T Consensus       161 afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          161 ALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            999999999999999999999999 999999998764

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.65  E-value=2.1e-16  Score=161.47  Aligned_cols=147  Identities=12%  Similarity=0.127  Sum_probs=109.4

Q ss_pred             cccccccCC-CCCChHHHHHhhcCCCcEE-EeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCC----
Q 003463           75 DDFDLRGLP-SSLEDLEDYDIFGSGGGME-LEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGE----  144 (818)
Q Consensus        75 ~e~~V~~Lp-~s~~E~el~diF~~~G~i~-V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~----  144 (818)
                      ..++|++|+ ..+++.+|+++|+.+|.|. |..-.   ..+|++||.|.+.+.|.    .+++..+.+....+...    
T Consensus         5 ~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~---~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK---SKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             SEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECT---TSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEec---CCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            679999999 8999999999999999983 32211   14799999999987554    23333333321111100    


Q ss_pred             ------------------------CC----------CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCE--EEEEeC---
Q 003463          145 ------------------------HP----------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDI--RTLYTA---  185 (818)
Q Consensus       145 ------------------------~~----------~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I--~~v~~~---  185 (818)
                                              ..          ....++++|||+|||.++|+++|+++|++||.|  ..+++.   
T Consensus        82 ~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~  161 (205)
T 3tyt_A           82 IMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK  161 (205)
T ss_dssp             CCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred             cCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC
Confidence                                    00          012356799999999999999999999999998  777742   


Q ss_pred             CCcccEEEEEEccHHHHHHHHHHhcCcccccc----ccccccc
Q 003463          186 CKHRGFVMISYYDIRAARTAMRALQNKPLRRR----KLDIHFS  224 (818)
Q Consensus       186 ~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr----~L~V~~a  224 (818)
                      ++.+|+|||+|.+.++|.+|+..|+|..|.|+    ++.|+++
T Consensus       162 ~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            34569999999999999999999999999876    4555543

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.63  E-value=7.6e-16  Score=162.51  Aligned_cols=146  Identities=15%  Similarity=0.127  Sum_probs=117.4

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE-EEeecCCCCCcccEEEEEecChhhcc----ccCccccCCCCccccCCCCCC
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  148 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i-~V~~d~~t~~skG~a~v~f~~~~~a~----~~~~~~l~n~~~~~~g~~~~~  148 (818)
                      .+.++|++||.++++.++.++|+.+|.| .|..    .+.+|++||.|.+.+.|.    .+++..+.+....+...    
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i----~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a----   93 (261)
T 3sde_A           22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI----NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA----   93 (261)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC----
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE----eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec----
Confidence            4679999999999999999999999987 2322    245799999999987654    23444444443333322    


Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcC-cccc---ccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQN-KPLR---RRKLD  220 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng-~~l~---gr~L~  220 (818)
                       .+.++|||+|||.++|+++|+++|+.||.|..|.+    +++++|||||+|.+.++|.+|++.|++ ..+.   +++|.
T Consensus        94 -~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 -THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             -CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             -ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence             35789999999999999999999999999999874    567899999999999999999999955 4443   89999


Q ss_pred             ccccCCCC
Q 003463          221 IHFSIPKD  228 (818)
Q Consensus       221 V~~a~pk~  228 (818)
                      |.++.+..
T Consensus       173 v~~~~~~~  180 (261)
T 3sde_A          173 VEPMEQFD  180 (261)
T ss_dssp             EEECCCEE
T ss_pred             EeeccccC
Confidence            99987654

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.62  E-value=7.8e-16  Score=139.21  Aligned_cols=75  Identities=28%  Similarity=0.488  Sum_probs=70.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..+|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+||+|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            458999999999999999999999999999975     466789999999999999999999999999999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.62  E-value=6.4e-16  Score=147.66  Aligned_cols=121  Identities=21%  Similarity=0.330  Sum_probs=77.3

Q ss_pred             cEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe
Q 003463          190 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  269 (818)
Q Consensus       190 G~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~  269 (818)
                      -++|++|.+...|..|+..+++....|+. .+.+..+    ........+|||+|||.++|+++|+++|++||.|..|++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~----~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i   79 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRP----PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI   79 (135)
T ss_dssp             -------------------------------CCSCCS----CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCC----CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE
Confidence            36788999999999999999887766553 2233332    233445679999999999999999999999999999976


Q ss_pred             -----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCccc
Q 003463          270 -----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       270 -----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r  315 (818)
                           ++.++|||||+|.+.++|++|++.|||..|.|++|+|++++++..+
T Consensus        80 ~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence                 4567899999999999999999999999999999999999876543

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.60  E-value=5.9e-16  Score=142.82  Aligned_cols=103  Identities=24%  Similarity=0.400  Sum_probs=92.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..++++|||+|||.++++++|+++|++||.|..|.+  .+.++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            346799999999999999999999999999999985  566799999999999999999999999999999999999976


Q ss_pred             CCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCC
Q 003463          227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE  263 (818)
Q Consensus       227 k~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~  263 (818)
                      +...            .+++...++++|.++|++||.
T Consensus        85 ~~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           85 NRAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             Chhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            4422            467778899999999999984

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.60  E-value=1.5e-15  Score=137.36  Aligned_cols=76  Identities=22%  Similarity=0.472  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|.+++
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            3579999999999999999999999999999873     57889999999999999999999999999999999999997


Q ss_pred             C
Q 003463          226 P  226 (818)
Q Consensus       226 p  226 (818)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.59  E-value=2.3e-15  Score=139.51  Aligned_cols=80  Identities=23%  Similarity=0.390  Sum_probs=71.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe---cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~---~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+|||+++|+++|+++|++||.|.+|++   .+.++|||||+|.+.++|++||+.|+|..|.|++|+|++++++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            458999999999999999999999999999876   23458999999999999999999999999999999999998866


Q ss_pred             ccc
Q 003463          314 ARR  316 (818)
Q Consensus       314 ~r~  316 (818)
                      .+.
T Consensus        85 ~~~   87 (115)
T 4f25_A           85 ERE   87 (115)
T ss_dssp             C--
T ss_pred             ccc
Confidence            543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.57  E-value=3.8e-15  Score=137.40  Aligned_cols=83  Identities=22%  Similarity=0.298  Sum_probs=75.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+.+++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|||..+.|+.|+|++++
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            3568999999999999999999999999999976     46778999999999999999999999999999999999998


Q ss_pred             CCcccchh
Q 003463          311 PGGARRNL  318 (818)
Q Consensus       311 ~~~~r~~~  318 (818)
                      .+..++.+
T Consensus        85 ~~~~~~~~   92 (110)
T 3s8s_A           85 KGQQRMKY   92 (110)
T ss_dssp             TTHHHHHH
T ss_pred             CCcHHHHH
Confidence            77655443

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.57  E-value=9.6e-15  Score=134.66  Aligned_cols=102  Identities=21%  Similarity=0.405  Sum_probs=90.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..++|||+|||..+++++|+++|++||.|..|++  ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+++++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            3568999999999999999999999999999987  45678999999999999999999999999999999999998765


Q ss_pred             ccchhhhccchhccHHHHHHHHhhcCCC
Q 003463          314 ARRNLMLQLNQELEQDESRILQHQVGSP  341 (818)
Q Consensus       314 ~r~~~~~ql~~~~~~~~l~~~f~~~GsP  341 (818)
                      ..    .++.....++++..+|.++|.+
T Consensus        87 ~~----~~~~~~~~~~~l~~~~~~~g~~  110 (115)
T 3lqv_A           87 AF----QKMDTKKKEEQLKLLKEKYGIN  110 (115)
T ss_dssp             HT----TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             hh----hhhhHhHhHHHHHHHHHHhCCC
Confidence            43    4556677888999999999854

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=4.3e-15  Score=133.86  Aligned_cols=94  Identities=24%  Similarity=0.364  Sum_probs=81.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD  232 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~  232 (818)
                      ++|||+|||.++|+++|+++|++||+|..|.+...++|||||+|.+.++|++|++.|++..+.|+.|.|.++.++.....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   80 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSR   80 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCccc
Confidence            58999999999999999999999999999986444799999999999999999999999999999999999987653322


Q ss_pred             C------CCCccceeeecCC
Q 003463          233 K------DLNQGTLVVFNLD  246 (818)
Q Consensus       233 ~------~~~~~tL~V~NLp  246 (818)
                      .      .....+|||+||+
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCCccccCCCceecCCCC
Confidence            1      1124689999997

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=1.9e-14  Score=129.03  Aligned_cols=81  Identities=27%  Similarity=0.393  Sum_probs=74.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            35679999999999999999999999999999987     5567899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            987643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.55  E-value=3.7e-15  Score=132.54  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=69.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccC-CeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcC-CCccCCceEEEEecC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN-RSDIAGKRIKLEPSR  310 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG-~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~Ln-G~~i~Gr~L~V~~a~  310 (818)
                      ++|||+|||+++|+++|+++|++|| .|++|++     ++.++|||||+|.+.++|++|++.++ +..+.|++|+|+|++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5899999999999999999999999 8998865     46789999999999999999999874 568999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.55  E-value=1.6e-14  Score=140.60  Aligned_cols=126  Identities=23%  Similarity=0.357  Sum_probs=95.1

Q ss_pred             EeecCCCCCcccEEEEEecChhhccccC----ccccCCC-------C-------ccccCCCCCCCCCCcEEEEcCCCCCC
Q 003463          103 LEGEPQESLSMSMSKISISDSASGNGLL----HYSVPNG-------A-------GTVAGEHPYGEHPSRTLFVRNINSNV  164 (818)
Q Consensus       103 V~~d~~t~~skG~a~v~f~~~~~a~~~~----~~~l~n~-------~-------~~~~g~~~~~e~~srtLfV~NLP~~v  164 (818)
                      |..+..  ..+||+||.|.+.+.|....    .....++       .       ............+.++|||+|||.++
T Consensus         5 l~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~   82 (158)
T 2kn4_A            5 LILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRT   82 (158)
T ss_dssp             EEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTC
T ss_pred             EEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCC
Confidence            444543  58899999999887654221    0000111       0       00011122233457899999999999


Q ss_pred             cHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCC
Q 003463          165 EDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  230 (818)
Q Consensus       165 TEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~  230 (818)
                      ++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.++...
T Consensus        83 ~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           83 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             CHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            99999999999999999984     5678999999999999999999999999999999999999876543

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=2.6e-14  Score=129.44  Aligned_cols=82  Identities=24%  Similarity=0.300  Sum_probs=74.8

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      .....+|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|+|..|.|++|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345679999999999999999999999999999976     456789999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      ++++..+
T Consensus        92 a~~~~~~   98 (105)
T 1x5u_A           92 ASAHNKN   98 (105)
T ss_dssp             TTTTSCC
T ss_pred             CCCCCcC
Confidence            9887644

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.8e-14  Score=131.92  Aligned_cols=82  Identities=23%  Similarity=0.309  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcC--cccccccccccccCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHFSIP  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng--~~l~gr~L~V~~a~p  226 (818)
                      ..+.++|||+|||+++||++|+++|++||+|.+|++.. .+|||||+|.+.++|++|++.|++  ..|.|++|+|.++.+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            34679999999999999999999999999999998643 489999999999999999998864  789999999999987


Q ss_pred             CCCCC
Q 003463          227 KDNPS  231 (818)
Q Consensus       227 k~~~~  231 (818)
                      +....
T Consensus        92 ~~~~~   96 (105)
T 1sjq_A           92 KELKT   96 (105)
T ss_dssp             SSCCC
T ss_pred             CCCCc
Confidence            76544

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.54  E-value=1.3e-14  Score=131.69  Aligned_cols=80  Identities=13%  Similarity=0.269  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcc--cccccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~--l~gr~L~V~~a~  225 (818)
                      ...|+++|||+|||.++|+++|+++|++||.|.++++. +.||||||+|.+.++|++|++.|++..  +.|++|+|.|+.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            34588999999999999999999999999999999863 468999999999999999999999876  789999999998


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      +++
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            754

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=2.4e-14  Score=128.29  Aligned_cols=82  Identities=26%  Similarity=0.395  Sum_probs=75.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            356899999999999999999999999999999985     567899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9887654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.54  E-value=3.4e-15  Score=132.73  Aligned_cols=79  Identities=22%  Similarity=0.409  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhc-Cccccccccccccc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ-NKPLRRRKLDIHFS  224 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG-~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Ln-g~~l~gr~L~V~~a  224 (818)
                      +++|||+|||.++||++|+++|++|| .|.+|++     +++++|||||+|.+.++|++|++.++ +..+.|++|+|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            57999999999999999999999999 7988873     57789999999999999999999874 56799999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .|+...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            887643

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.54  E-value=1.7e-14  Score=133.09  Aligned_cols=79  Identities=18%  Similarity=0.385  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||+++++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            356899999999999999999999999999999984     578999999999999999999999999999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8643

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=3e-14  Score=128.03  Aligned_cols=81  Identities=25%  Similarity=0.354  Sum_probs=73.8

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....++|||+|||..+|+++|+++|++||.|..|++.    +.++|||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            3456799999999999999999999999999999763    456799999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      +++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            98764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=3.7e-14  Score=128.77  Aligned_cols=83  Identities=23%  Similarity=0.441  Sum_probs=74.8

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec------CCCCceEEEEEcCHHHHHHHHHHc-CCCccCCceEE
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIK  305 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~------g~srG~aFVeF~d~e~A~~Ai~~L-nG~~i~Gr~L~  305 (818)
                      ......+|||+|||..+++++|+++|++||.|..|++.      +.++|||||+|.+.++|.+|++.| |+..|.|++|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            34456799999999999999999999999999999873      445899999999999999999999 99999999999


Q ss_pred             EEecCCCccc
Q 003463          306 LEPSRPGGAR  315 (818)
Q Consensus       306 V~~a~~~~~r  315 (818)
                      |++++++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999887643

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.54  E-value=1e-14  Score=143.58  Aligned_cols=122  Identities=18%  Similarity=0.279  Sum_probs=72.5

Q ss_pred             EEEccHHHHHHHHHHhcCcccc--cccccccccCCCC---------------C-CCCCCCCccceeeecCCCCCCHHHHH
Q 003463          194 ISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIPKD---------------N-PSDKDLNQGTLVVFNLDPSVSNEDLR  255 (818)
Q Consensus       194 V~F~d~e~A~~Al~~Lng~~l~--gr~L~V~~a~pk~---------------~-~~~~~~~~~tL~V~NLp~~vteedL~  255 (818)
                      .+|.+.++|+.|+..+++....  |+.+.........               . .........+|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6889999999999988887665  5555444321100               0 01122334689999999999999999


Q ss_pred             HHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCccc
Q 003463          256 QIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       256 ~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r  315 (818)
                      ++|++||.|..|++     ++.++|||||+|.+.++|.+||..|||..|.|+.|+|.|+.++..+
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            99999999999976     3446899999999999999999999999999999999999876644

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=3.6e-14  Score=129.67  Aligned_cols=81  Identities=30%  Similarity=0.469  Sum_probs=73.4

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ....++|||+|||.++|+++|+++|++||.|..|++  ++.+++||||+|.+.++|++|++.||+..|.|++|+|+++++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            345679999999999999999999999999999876  344689999999999999999999999999999999999988


Q ss_pred             Ccc
Q 003463          312 GGA  314 (818)
Q Consensus       312 ~~~  314 (818)
                      +..
T Consensus        99 ~~~  101 (109)
T 1x4a_A           99 GRG  101 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.2e-14  Score=132.99  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=71.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCC--CccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG--~~i~Gr~L~V~~a~~~~  313 (818)
                      ...+|||+|||+++|+++|+++|++||.|++|++.. .||||||+|.+.++|++|++.|++  ..|.|++|+|+|++++.
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            456899999999999999999999999999999864 489999999999999999998864  78999999999998876


Q ss_pred             cc
Q 003463          314 AR  315 (818)
Q Consensus       314 ~r  315 (818)
                      .+
T Consensus        94 ~~   95 (105)
T 1sjq_A           94 LK   95 (105)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.53  E-value=2.1e-14  Score=130.32  Aligned_cols=77  Identities=21%  Similarity=0.248  Sum_probs=70.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCc--cCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~--i~Gr~L~V~~a~~~~  313 (818)
                      ..++|||+|||.++|+++|+++|++||.|.+|++. +.||+|||+|.+.++|.+|++.|++..  +.|++|+|+||+++.
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            45789999999999999999999999999999885 468999999999999999999999886  789999999998754

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.53  E-value=1.9e-14  Score=125.55  Aligned_cols=77  Identities=18%  Similarity=0.390  Sum_probs=69.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            3568999999999999999999999999999976     44568999999999999999999999999999999999998


Q ss_pred             CC
Q 003463          311 PG  312 (818)
Q Consensus       311 ~~  312 (818)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.1e-14  Score=128.61  Aligned_cols=84  Identities=21%  Similarity=0.332  Sum_probs=75.5

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ......+|||+|||+.+|+++|+++|++||.|..|++.   +..++||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            34466799999999999999999999999999999763   467899999999999999999999999999999999999


Q ss_pred             CCCcccc
Q 003463          310 RPGGARR  316 (818)
Q Consensus       310 ~~~~~r~  316 (818)
                      +++..+.
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=5.2e-14  Score=126.22  Aligned_cols=82  Identities=23%  Similarity=0.470  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ |++..|.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            3457899999999999999999999999999999985     46689999999999999999999 99999999999999


Q ss_pred             ccCCCCCC
Q 003463          223 FSIPKDNP  230 (818)
Q Consensus       223 ~a~pk~~~  230 (818)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99877654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.53  E-value=1.7e-14  Score=127.34  Aligned_cols=73  Identities=18%  Similarity=0.192  Sum_probs=69.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..-|||+||++.+|+++|+++|.+||+|+++++. .++|||||+|.+.++|.+|++.||+..+.|++|+|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~-~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY-LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEc-CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4579999999999999999999999999999985 479999999999999999999999999999999999983

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.7e-14  Score=127.75  Aligned_cols=84  Identities=15%  Similarity=0.295  Sum_probs=76.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34567899999999999999999999999999999984     5678999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999876543

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=5.5e-14  Score=127.02  Aligned_cols=83  Identities=30%  Similarity=0.403  Sum_probs=74.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecC---CCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g---~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....++|||+|||..+++++|+++|++||.|..|++..   .++|||||+|.+.++|++|++.|+|..+.|++|+|++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            34567999999999999999999999999999997633   357999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 003463          311 PGGARR  316 (818)
Q Consensus       311 ~~~~r~  316 (818)
                      ++..++
T Consensus        92 ~~~~~~   97 (103)
T 2cqi_A           92 TPSSQK   97 (103)
T ss_dssp             CTTCCC
T ss_pred             CCcccc
Confidence            876543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.52  E-value=2.1e-14  Score=132.79  Aligned_cols=90  Identities=19%  Similarity=0.128  Sum_probs=71.7

Q ss_pred             ccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccC-CeEEEEec-CCCCceEEEEEcCHHHHHHHHHHc
Q 003463          217 RKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRET-PHKRHHKFIEFYDVRAAEAALKSL  294 (818)
Q Consensus       217 r~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG-~I~~vr~~-g~srG~aFVeF~d~e~A~~Ai~~L  294 (818)
                      .++.+.|+.+..       ...+|||+|||+++++++|+++|++|| .|..+++. ..++|||||+|.+.++|++||+.|
T Consensus        15 ~~~~~~~~~~p~-------~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~l   87 (111)
T 2jvr_A           15 VPRGSHMSKLPA-------KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERL   87 (111)
T ss_dssp             ----------CC-------CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHT
T ss_pred             eecchhcCCCCC-------CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHc
Confidence            345566654322       356899999999999999999999999 99999883 568999999999999999999999


Q ss_pred             CCCccCCceEEEEecCCCc
Q 003463          295 NRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       295 nG~~i~Gr~L~V~~a~~~~  313 (818)
                      ||.++.|++|+|++++.+.
T Consensus        88 ng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           88 NNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             TTEEETTEEEEEEESCC--
T ss_pred             CCCEECCeEEEEEECCCCC
Confidence            9999999999999997654

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=2.9e-14  Score=133.43  Aligned_cols=91  Identities=24%  Similarity=0.333  Sum_probs=77.1

Q ss_pred             ccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcC--ccccccc
Q 003463          141 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRK  218 (818)
Q Consensus       141 ~~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng--~~l~gr~  218 (818)
                      ..+.......++++|||+|||+++||++|+++|++||.|..|++. +.+|||||+|.+.++|++|++.+++  ..|.|++
T Consensus        20 ~~~~~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~-~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~   98 (119)
T 2ad9_A           20 HMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   98 (119)
T ss_dssp             --CCTTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEE-GGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBC
T ss_pred             ccccccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhccCCceECCeE
Confidence            344444556688999999999999999999999999999999864 3589999999999999999998874  6899999


Q ss_pred             ccccccCCCCCCCC
Q 003463          219 LDIHFSIPKDNPSD  232 (818)
Q Consensus       219 L~V~~a~pk~~~~~  232 (818)
                      |+|.++.++.....
T Consensus        99 l~V~~a~~k~~~~~  112 (119)
T 2ad9_A           99 IYIQFSNHKELKTD  112 (119)
T ss_dssp             CEEEECSSSSCCCC
T ss_pred             EEEEEccCCCCCcc
Confidence            99999987765443

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.52  E-value=1e-14  Score=131.23  Aligned_cols=76  Identities=22%  Similarity=0.396  Sum_probs=68.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCC--eEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCC----ccCCceE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGE--VKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS----DIAGKRI  304 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~--I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~----~i~Gr~L  304 (818)
                      .-.||||+|||+++|+++|+++|++||.  |.+|++     ++.++|||||+|.+.++|++|++.|||.    .|+||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            4468999999999999999999999995  567764     4678999999999999999999999997    4899999


Q ss_pred             EEEecCC
Q 003463          305 KLEPSRP  311 (818)
Q Consensus       305 ~V~~a~~  311 (818)
                      +|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999975

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.52  E-value=3e-14  Score=123.19  Aligned_cols=76  Identities=22%  Similarity=0.297  Sum_probs=70.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      .+|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            47999999999999999999999999999875     3556899999999999999999999999999999999999876


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=3.6e-14  Score=128.21  Aligned_cols=82  Identities=21%  Similarity=0.321  Sum_probs=74.4

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            445679999999999999999999999999999976     445688999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9887643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3.6e-14  Score=128.21  Aligned_cols=84  Identities=26%  Similarity=0.386  Sum_probs=76.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      +....+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..|.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            334567899999999999999999999999999999984     367899999999999999999999999999999999


Q ss_pred             ccccCCCCC
Q 003463          221 IHFSIPKDN  229 (818)
Q Consensus       221 V~~a~pk~~  229 (818)
                      |.++.++..
T Consensus        87 V~~a~~~~~   95 (103)
T 2dnm_A           87 VQVARYGRR   95 (103)
T ss_dssp             EEECSSCCS
T ss_pred             EEECCcCCC
Confidence            999987654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.52  E-value=4.9e-14  Score=124.42  Aligned_cols=81  Identities=19%  Similarity=0.282  Sum_probs=74.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            356799999999999999999999999999999874   56689999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003463          226 PKDN  229 (818)
Q Consensus       226 pk~~  229 (818)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7654

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=6.4e-14  Score=125.32  Aligned_cols=78  Identities=21%  Similarity=0.374  Sum_probs=72.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC--CceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA--GKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~--Gr~L~V~~a~~~~  313 (818)
                      ..++|||+|||..+|+++|+++|++||.|..|++... ++||||+|.+.++|++|++.|||..+.  |++|+|++++++.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            4568999999999999999999999999999988643 899999999999999999999999999  9999999999875


Q ss_pred             c
Q 003463          314 A  314 (818)
Q Consensus       314 ~  314 (818)
                      .
T Consensus        95 ~   95 (97)
T 1why_A           95 S   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.3e-14  Score=125.39  Aligned_cols=78  Identities=26%  Similarity=0.442  Sum_probs=71.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      .....+|||+|||..+++++|+++|++||.|..|++.     +..+|||||+|.+.++|.+|++.|||..+.|++|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456799999999999999999999999999999763     55688999999999999999999999999999999999


Q ss_pred             cCC
Q 003463          309 SRP  311 (818)
Q Consensus       309 a~~  311 (818)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            976

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.52  E-value=3.1e-14  Score=131.39  Aligned_cols=81  Identities=25%  Similarity=0.417  Sum_probs=73.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45579999999999999999999999999999875     4556789999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpz_A          103 RSKNDS  108 (115)
T ss_dssp             CCSCCC
T ss_pred             CCCCcC
Confidence            987643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=5.8e-14  Score=125.95  Aligned_cols=80  Identities=23%  Similarity=0.449  Sum_probs=73.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++ |++..+.|+.|+|+++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            45679999999999999999999999999999986     35578999999999999999998 9999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            987643

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=5.7e-14  Score=128.35  Aligned_cols=82  Identities=15%  Similarity=0.232  Sum_probs=72.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCc--cccccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK--PLRRRKLDIHFS  224 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~--~l~gr~L~V~~a  224 (818)
                      ....++++|||+|||.++++++|+++|++||.|..|.+. +.+|||||+|.+.++|++|++.|++.  .+.|++|+|.|+
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            345678999999999999999999999999999999864 35899999999999999999988765  489999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        89 ~~~~~   93 (104)
T 1wex_A           89 TSKRI   93 (104)
T ss_dssp             SSSSC
T ss_pred             cCccc
Confidence            87654

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=6.2e-14  Score=127.45  Aligned_cols=80  Identities=15%  Similarity=0.176  Sum_probs=71.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc--CCCccCCceEEEEecCCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~~  312 (818)
                      ...++|||+|||+++++++|+++|++||.|.+|++.. .+|||||+|.+.++|.+|++.|  ++..+.|++|+|.|++++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            3457999999999999999999999999999998754 4899999999999999999987  467899999999999877


Q ss_pred             ccc
Q 003463          313 GAR  315 (818)
Q Consensus       313 ~~r  315 (818)
                      ..+
T Consensus        92 ~~~   94 (101)
T 2cq1_A           92 ELK   94 (101)
T ss_dssp             SCC
T ss_pred             cCc
Confidence            644

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.51  E-value=3.2e-14  Score=126.98  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      |+++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            5789999999999999999999999999999984     36779999999999999999999999999999999999998


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=5.9e-14  Score=127.44  Aligned_cols=83  Identities=25%  Similarity=0.490  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEEccHHHHHHHHHHh-cCccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLD  220 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~d~e~A~~Al~~L-ng~~l~gr~L~  220 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.| ++..|.|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4457899999999999999999999999999999985      4557999999999999999999999 99999999999


Q ss_pred             ccccCCCCCC
Q 003463          221 IHFSIPKDNP  230 (818)
Q Consensus       221 V~~a~pk~~~  230 (818)
                      |.++.++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.51  E-value=5.4e-14  Score=129.60  Aligned_cols=82  Identities=21%  Similarity=0.410  Sum_probs=74.3

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      .....+|||+|||..+++++|+++|++||.|..|++     ++..+|||||+|.+.++|++|++.|+|..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999976     445689999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      ++++..+
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9887643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=4.9e-14  Score=124.27  Aligned_cols=77  Identities=26%  Similarity=0.416  Sum_probs=72.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ...++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|++++++..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            356799999999999999999999999999999986   78999999999999999999999999999999999988764

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.51  E-value=3.8e-14  Score=123.11  Aligned_cols=75  Identities=27%  Similarity=0.462  Sum_probs=69.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.|||..+.|++|+|++++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            4579999999999999999999999999999975     34568999999999999999999999999999999999985

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=5.7e-14  Score=124.75  Aligned_cols=81  Identities=23%  Similarity=0.444  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .++++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46799999999999999999999999999999984     4668999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=5.6e-14  Score=124.81  Aligned_cols=79  Identities=27%  Similarity=0.388  Sum_probs=72.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            3568999999999999999999999999999976     35568999999999999999999999999999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ++..
T Consensus        84 ~~~~   87 (95)
T 2dnz_A           84 ERLD   87 (95)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            8654

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=7.7e-14  Score=127.48  Aligned_cols=84  Identities=17%  Similarity=0.311  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|++  .++++|||||+|.+.++|++|++.|++..|.|+.|+|.++
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            34456799999999999999999999999999999885  4557899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4a_A           97 RSGRGT  102 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=6.5e-14  Score=125.84  Aligned_cols=82  Identities=16%  Similarity=0.295  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.|++|+|.+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999884    467789999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003463          224 SIPKDN  229 (818)
Q Consensus       224 a~pk~~  229 (818)
                      +.++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            987653

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=4.5e-14  Score=127.58  Aligned_cols=83  Identities=22%  Similarity=0.450  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            4457899999999999999999999999999999884     56789999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 003463          223 FSIPKDNP  230 (818)
Q Consensus       223 ~a~pk~~~  230 (818)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99876543

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.51  E-value=2.9e-14  Score=124.43  Aligned_cols=78  Identities=18%  Similarity=0.403  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35789999999999999999999999999999884     5668999999999999999999999999999999999998


Q ss_pred             CCC
Q 003463          225 IPK  227 (818)
Q Consensus       225 ~pk  227 (818)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=8.6e-14  Score=123.35  Aligned_cols=76  Identities=29%  Similarity=0.430  Sum_probs=70.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||..+++++|+++|++||.|..|++.     +.+++||||+|.+.++|++|++.|||..+.|++|+|+|+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            456799999999999999999999999999999763     456899999999999999999999999999999999998


Q ss_pred             C
Q 003463          310 R  310 (818)
Q Consensus       310 ~  310 (818)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=4.9e-14  Score=126.04  Aligned_cols=81  Identities=25%  Similarity=0.452  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--------CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--------~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      .+.++|||+|||.++++++|+++|++||.|..|.+        +++++|||||+|.+.++|++|++.|++..|.|++|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            46799999999999999999999999999999874        2277899999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.51  E-value=8e-14  Score=128.46  Aligned_cols=84  Identities=17%  Similarity=0.381  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34457899999999999999999999999999999884     5667999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (115)
T 2dgo_A           90 NWATRKPPA   98 (115)
T ss_dssp             EESSCCCCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=4.7e-14  Score=127.43  Aligned_cols=80  Identities=28%  Similarity=0.432  Sum_probs=73.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            356799999999999999999999999999999763     567899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87653

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.51  E-value=3.6e-14  Score=122.69  Aligned_cols=77  Identities=27%  Similarity=0.458  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      +.+|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            468999999999999999999999999999874     467799999999999999999999999999999999999987


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=6.3e-14  Score=126.63  Aligned_cols=84  Identities=18%  Similarity=0.404  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|++..|.|+.|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            3457899999999999999999999999999999884   4578999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 003463          225 IPKDNPS  231 (818)
Q Consensus       225 ~pk~~~~  231 (818)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            8876543

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=6.1e-14  Score=125.54  Aligned_cols=79  Identities=25%  Similarity=0.413  Sum_probs=72.0

Q ss_pred             CccceeeecCCCCCCHHHHH----HHhhccCCeEEEEecCC--CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRETPH--KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~----~lFs~fG~I~~vr~~g~--srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...+|||+|||..+++++|+    ++|++||.|.+|++...  .++||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            45689999999999999999    99999999999987422  2899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      +++..
T Consensus        88 ~~~~~   92 (96)
T 2dgx_A           88 TGASG   92 (96)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.51  E-value=6.7e-14  Score=126.75  Aligned_cols=82  Identities=20%  Similarity=0.266  Sum_probs=73.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC---ceEEEE
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG---KRIKLE  307 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G---r~L~V~  307 (818)
                      ....+|||+|||..+++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..+.|   +.|+|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            34679999999999999999999999999999976    34457999999999999999999999999998   999999


Q ss_pred             ecCCCcccc
Q 003463          308 PSRPGGARR  316 (818)
Q Consensus       308 ~a~~~~~r~  316 (818)
                      +++++..++
T Consensus        93 ~a~~~~~~~  101 (105)
T 2dnh_A           93 FADTDKESG  101 (105)
T ss_dssp             ESCSSCCCS
T ss_pred             ECccCcccC
Confidence            999876543

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=9.5e-14  Score=126.90  Aligned_cols=81  Identities=20%  Similarity=0.363  Sum_probs=74.2

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcC------CCccCCce
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLN------RSDIAGKR  303 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~Ln------G~~i~Gr~  303 (818)
                      ...++|||+|||..+|+++|+++|++||.|..|++.     +.++|||||+|.+.++|.+|++.||      +..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            346799999999999999999999999999999763     5678999999999999999999999      99999999


Q ss_pred             EEEEecCCCccc
Q 003463          304 IKLEPSRPGGAR  315 (818)
Q Consensus       304 L~V~~a~~~~~r  315 (818)
                      |+|.+++++..+
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999987644

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.50  E-value=4.1e-14  Score=123.63  Aligned_cols=79  Identities=24%  Similarity=0.396  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecC-----C-CCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP-----H-KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g-----~-srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ..++|||+|||.++|+++|+++|++||.|..+++..     . .+|+|||+|.+.++|.+|++.|||..+.|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            346899999999999999999999999999997621     2 6899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      ++...
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.50  E-value=5.8e-14  Score=125.35  Aligned_cols=79  Identities=18%  Similarity=0.275  Sum_probs=72.8

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      .++|||+|||..+++++|+++|++||.|.+|++     ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|+++++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            358999999999999999999999999999976     356689999999999999999999999999999999999998


Q ss_pred             Cccc
Q 003463          312 GGAR  315 (818)
Q Consensus       312 ~~~r  315 (818)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7643

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.50  E-value=3.7e-14  Score=129.94  Aligned_cols=95  Identities=20%  Similarity=0.298  Sum_probs=80.9

Q ss_pred             ccccccccccCCCCCCCCCCCCccceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHH
Q 003463          215 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       215 ~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~  293 (818)
                      .|.+|.+..+.+..... .....++|||+|||.. +++++|+++|++||.|..|++   +++||||+|.+.++|++|++.
T Consensus         6 ~g~~~~~~~s~~~~~~~-~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~   81 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKND-PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLG   81 (110)
T ss_dssp             CSCCCCCCCCCSCCSCC-CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHH
T ss_pred             CCcccccccCCCCCCCC-CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHH
Confidence            45667777665443322 2334579999999999 999999999999999999998   589999999999999999999


Q ss_pred             cCCCccCCceEEEEecCCCc
Q 003463          294 LNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       294 LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      |+|..+.|++|+|++++++.
T Consensus        82 l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           82 ENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HTTCEETTEECCEEESCCCC
T ss_pred             cCCCEECCeEEEEEECCCCC
Confidence            99999999999999998654

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.50  E-value=9.1e-14  Score=129.07  Aligned_cols=79  Identities=28%  Similarity=0.448  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..++|||+|||.++|+++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4568999999999999999999999999999976    455689999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003463          312 GGA  314 (818)
Q Consensus       312 ~~~  314 (818)
                      +..
T Consensus        86 ~~~   88 (116)
T 2fy1_A           86 PSF   88 (116)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=4e-14  Score=127.56  Aligned_cols=81  Identities=22%  Similarity=0.481  Sum_probs=73.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|.+|++.|||..|.|++|+|+++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            345799999999999999999999999999999763     446899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 1x5s_A           90 GKSSDN   95 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            887643

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=7.7e-14  Score=126.86  Aligned_cols=83  Identities=22%  Similarity=0.299  Sum_probs=73.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhc--Cccccccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLDIHFS  224 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Ln--g~~l~gr~L~V~~a  224 (818)
                      ....++++|||+|||.++++++|+++|++||.|..|.+.. .+|||||+|.+.++|++|++.|+  +..+.|++|+|.|+
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            3445789999999999999999999999999999998643 48999999999999999999875  57799999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .++...
T Consensus        89 ~~~~~~   94 (101)
T 2cq1_A           89 NHKELK   94 (101)
T ss_dssp             SCSSCC
T ss_pred             CcccCc
Confidence            876543

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=5.8e-14  Score=128.30  Aligned_cols=79  Identities=19%  Similarity=0.234  Sum_probs=71.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCC--ccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~--~i~Gr~L~V~~a~~~~  313 (818)
                      ..++|||+|||+++++++|+++|++||.|.+|++.. .||||||+|.+.++|.+|++.|++.  .+.|++|+|+|++++.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcc
Confidence            457999999999999999999999999999998754 4899999999999999999998765  5999999999998765


Q ss_pred             cc
Q 003463          314 AR  315 (818)
Q Consensus       314 ~r  315 (818)
                      .+
T Consensus        93 ~~   94 (104)
T 1wex_A           93 IT   94 (104)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1.2e-13  Score=124.80  Aligned_cols=82  Identities=21%  Similarity=0.362  Sum_probs=73.9

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecC---CCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g---~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....++|||+|||.++++++|+++|++||.|..|++..   .+++||||+|.+.++|++|++.|||..|.|+.|+|++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   91 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            34567999999999999999999999999999998742   358999999999999999999999999999999999998


Q ss_pred             CCccc
Q 003463          311 PGGAR  315 (818)
Q Consensus       311 ~~~~r  315 (818)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2cq3_A           92 ARVMT   96 (103)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            87643

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=4.3e-14  Score=128.27  Aligned_cols=79  Identities=25%  Similarity=0.412  Sum_probs=72.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||..+++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            345789999999999999999999999999999763     556899999999999999999999999999999999999


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      +++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8765

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.50  E-value=1.4e-14  Score=164.20  Aligned_cols=145  Identities=24%  Similarity=0.356  Sum_probs=103.4

Q ss_pred             HHHHhhcCCCEEEEEe-------CCCcccEE-----EEEEccHHHHHHHHHHhcCcccccc-----------cc--cccc
Q 003463          169 LRALFEQYGDIRTLYT-------ACKHRGFV-----MISYYDIRAARTAMRALQNKPLRRR-----------KL--DIHF  223 (818)
Q Consensus       169 Lr~lFs~fG~I~~v~~-------~~ksrG~A-----FV~F~d~e~A~~Al~~Lng~~l~gr-----------~L--~V~~  223 (818)
                      |..+|..+|+|..|..       ..+..+|+     |+.|.+..++..++..++......+           .+  .+..
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~~   88 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKM   88 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            7889999999887731       11233444     7778776655544433222221111           00  1111


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       224 a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ..+............+|||+|||+.+|+++|+++|++||.|+.|++     ++.++|||||+|.+.++|.+||..|||..
T Consensus        89 ~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  168 (437)
T 3pgw_S           89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK  168 (437)
T ss_pred             cCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE
Confidence            2222222223334579999999999999999999999999999976     45679999999999999999999999999


Q ss_pred             cCCceEEEEecCCCc
Q 003463          299 IAGKRIKLEPSRPGG  313 (818)
Q Consensus       299 i~Gr~L~V~~a~~~~  313 (818)
                      |.|+.|.|.++++..
T Consensus       169 i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          169 IDGRRVLVDVERGRT  183 (437)
T ss_pred             ECCEEEEEEEeCCCC
Confidence            999999999998754

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.50  E-value=5.8e-14  Score=128.35  Aligned_cols=81  Identities=23%  Similarity=0.390  Sum_probs=73.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|+..|||..+.|++|+|+++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            45578999999999999999999999999999976     3456899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus       104 ~~~~~~  109 (110)
T 1oo0_B          104 FVKGPK  109 (110)
T ss_dssp             EESSCC
T ss_pred             ccCCCC
Confidence            877644

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=4.2e-14  Score=126.49  Aligned_cols=79  Identities=23%  Similarity=0.359  Sum_probs=71.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEec--------CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~--------g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      ..++|||+|||.++++++|+++|++||.|..|++.        +.++|||||+|.+.++|++|++.|||..+.|++|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            35689999999999999999999999999998763        2567899999999999999999999999999999999


Q ss_pred             ecCCCcc
Q 003463          308 PSRPGGA  314 (818)
Q Consensus       308 ~a~~~~~  314 (818)
                      +++++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9988654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.50  E-value=1e-13  Score=125.58  Aligned_cols=82  Identities=20%  Similarity=0.340  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccc---ccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR---RKLDI  221 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g---r~L~V  221 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.+   +.|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            346899999999999999999999999999999884    45679999999999999999999999999998   99999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876643

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.50  E-value=4.9e-14  Score=122.43  Aligned_cols=77  Identities=26%  Similarity=0.480  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|++..+.|++|+|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346799999999999999999999999999999984     456899999999999999999999999999999999998


Q ss_pred             cC
Q 003463          224 SI  225 (818)
Q Consensus       224 a~  225 (818)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.50  E-value=5.5e-14  Score=129.70  Aligned_cols=84  Identities=15%  Similarity=0.347  Sum_probs=76.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999999998874     5678999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpz_A          100 QLKRSKNDS  108 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EEcCCCCcC
Confidence            999877653

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=9.1e-14  Score=125.56  Aligned_cols=83  Identities=18%  Similarity=0.429  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++   ...++|||||+|.+.++|++|++.|++..|.|+.|+|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            4467899999999999999999999999999999984   2346899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cqi_A           91 TTPSSQ   96 (103)
T ss_dssp             CCTTCC
T ss_pred             CCCccc
Confidence            876543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=5.7e-14  Score=125.72  Aligned_cols=79  Identities=19%  Similarity=0.221  Sum_probs=71.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ....+|||+|||..+++++|+++|++||.|....+++.++|||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            3457999999999999999999999999996333456789999999999999999999999999999999999998865

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=9.3e-14  Score=122.52  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|++..+.|++|+|.++.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   81 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKS   81 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCC
Confidence            3567999999999999999999999999999999864   7999999999999999999999999999999999998766


Q ss_pred             CC
Q 003463          229 NP  230 (818)
Q Consensus       229 ~~  230 (818)
                      ..
T Consensus        82 ~~   83 (90)
T 2dnq_A           82 KA   83 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.2e-14  Score=132.34  Aligned_cols=80  Identities=15%  Similarity=0.208  Sum_probs=72.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCC--CccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG--~~i~Gr~L~V~~a~~~~  313 (818)
                      ..++|||+|||+++|+++|+++|++||.|++|++.. .+|||||+|.+.++|.+|++.|++  ..|.|++|+|.|++++.
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~-~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCC
Confidence            457899999999999999999999999999998753 489999999999999999999984  68999999999998876


Q ss_pred             ccc
Q 003463          314 ARR  316 (818)
Q Consensus       314 ~r~  316 (818)
                      .+.
T Consensus       109 ~~~  111 (119)
T 2ad9_A          109 LKT  111 (119)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.4e-13  Score=124.41  Aligned_cols=84  Identities=21%  Similarity=0.369  Sum_probs=75.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|++   ...++|||||+|.+.++|++|++.|++..|.|+.|+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34456799999999999999999999999999999985   234689999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9876643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=5.7e-14  Score=126.56  Aligned_cols=81  Identities=26%  Similarity=0.443  Sum_probs=73.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            35679999999999999999999999999999976     3457899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887644

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=4.5e-14  Score=128.65  Aligned_cols=79  Identities=14%  Similarity=0.158  Sum_probs=71.5

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCc--ccccccccccccC
Q 003463          149 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK--PLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~--~l~gr~L~V~~a~  225 (818)
                      ..++++|||+|||+ ++|+++|+++|++||.|.+|++. +.+|||||+|.+.++|++|++.|++.  .|.|++|+|.++.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   90 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   90 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECC
Confidence            45789999999999 99999999999999999999864 45799999999999999999999865  4999999999998


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      ...
T Consensus        91 ~~~   93 (102)
T 1x4d_A           91 KYK   93 (102)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            654

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=1e-13  Score=126.63  Aligned_cols=83  Identities=20%  Similarity=0.460  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhc------Cccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ------NKPLRR  216 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Ln------g~~l~g  216 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+      +..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            4457899999999999999999999999999999984     35789999999999999999999999      999999


Q ss_pred             ccccccccCCCCCC
Q 003463          217 RKLDIHFSIPKDNP  230 (818)
Q Consensus       217 r~L~V~~a~pk~~~  230 (818)
                      +.|+|.++.++...
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999877543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=9e-14  Score=123.09  Aligned_cols=78  Identities=26%  Similarity=0.410  Sum_probs=72.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ....++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|.+|++.|||..+.|+.|+|++++++.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            3456799999999999999999999999999999986   5699999999999999999999999999999999998865


Q ss_pred             c
Q 003463          314 A  314 (818)
Q Consensus       314 ~  314 (818)
                      .
T Consensus        84 ~   84 (92)
T 2dgt_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            4

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=5.1e-14  Score=127.77  Aligned_cols=81  Identities=17%  Similarity=0.448  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...++++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..+.|+.|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            3456789999999999999999999999999999984     36789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      ++.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            997654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=9.6e-14  Score=122.42  Aligned_cols=78  Identities=28%  Similarity=0.409  Sum_probs=72.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      .....+|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            3456799999999999999999999999999999986   5699999999999999999999999999999999998765


Q ss_pred             c
Q 003463          314 A  314 (818)
Q Consensus       314 ~  314 (818)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.49  E-value=1.6e-14  Score=127.73  Aligned_cols=76  Identities=17%  Similarity=0.232  Sum_probs=65.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccC--CeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG--~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      .+|||+|||.++|+++|+++|++||  .|.++++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  8988864     56778999999999999999999999999999999999998


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            765

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.49  E-value=3.4e-14  Score=126.61  Aligned_cols=82  Identities=21%  Similarity=0.335  Sum_probs=75.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      .....+|||+|||..+++++|+++|++||.|..++.++.++|||||+|.+.++|.+|++.|+|..+.|++|+|++++++.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            34567999999999999999999999999998887777889999999999999999999999999999999999998876


Q ss_pred             cc
Q 003463          314 AR  315 (818)
Q Consensus       314 ~r  315 (818)
                      .+
T Consensus        93 ~~   94 (96)
T 1fjc_A           93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=5.2e-14  Score=128.27  Aligned_cols=77  Identities=17%  Similarity=0.236  Sum_probs=69.9

Q ss_pred             CccceeeecCCC-CCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCC--ccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~-~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~--~i~Gr~L~V~~a~~~  312 (818)
                      ...+|||+|||+ ++|++||+++|++||.|.+|++. ..++||||+|.+.++|.+|++.|++.  .|.|++|+|.+++..
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            457899999999 99999999999999999999985 35799999999999999999999865  599999999999864


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        93 ~   93 (102)
T 1x4d_A           93 K   93 (102)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.49  E-value=9.2e-14  Score=126.08  Aligned_cols=82  Identities=17%  Similarity=0.359  Sum_probs=74.0

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCcc---CCceEE
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI---AGKRIK  305 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i---~Gr~L~  305 (818)
                      .....+|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.|||..+   .|++|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            345679999999999999999999999999999976     355789999999999999999999999988   899999


Q ss_pred             EEecCCCccc
Q 003463          306 LEPSRPGGAR  315 (818)
Q Consensus       306 V~~a~~~~~r  315 (818)
                      |++++++..+
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999887643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.49  E-value=5.9e-14  Score=123.89  Aligned_cols=79  Identities=19%  Similarity=0.245  Sum_probs=72.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe---cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~---~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ...+|||+|||.++++++|+++|++||.|..|++   ++.++|||||+|.+.++|++|++.|+|..+.|++|+|+++++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4579999999999999999999999999999876   4456899999999999999999999999999999999999886


Q ss_pred             cc
Q 003463          313 GA  314 (818)
Q Consensus       313 ~~  314 (818)
                      ..
T Consensus        87 ~~   88 (92)
T 2dgv_A           87 SG   88 (92)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.49  E-value=5.1e-14  Score=129.20  Aligned_cols=80  Identities=24%  Similarity=0.436  Sum_probs=72.8

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      .....++|||+|||.++|+++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..+.|+.|+|++++++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            34566799999999999999999999999999999986   899999999999999999999999999999999999887


Q ss_pred             ccc
Q 003463          313 GAR  315 (818)
Q Consensus       313 ~~r  315 (818)
                      ..+
T Consensus       104 ~~r  106 (108)
T 2jvo_A          104 AKR  106 (108)
T ss_dssp             C--
T ss_pred             CCC
Confidence            643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.6e-14  Score=125.58  Aligned_cols=80  Identities=21%  Similarity=0.387  Sum_probs=72.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEE-Ee-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v-r~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ..++|||+|||..+++++|+++|++||.|..+ ++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35689999999999999999999999999887 65     3456899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887644

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=1.2e-13  Score=124.88  Aligned_cols=82  Identities=22%  Similarity=0.398  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhc-CCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcc-ccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQ-YGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKP-LRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~-fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~-l~gr~L~V~  222 (818)
                      ..+.++|||+|||.++++++|+++|++ ||.|..|++    +++++|||||+|.+.++|++|++.|++.. +.|+.|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            456799999999999999999999999 999999885    56789999999999999999999999999 999999999


Q ss_pred             ccCCCCCC
Q 003463          223 FSIPKDNP  230 (818)
Q Consensus       223 ~a~pk~~~  230 (818)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99876543

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=9.3e-14  Score=124.23  Aligned_cols=79  Identities=27%  Similarity=0.477  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccc--cccccccccCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIP  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~--gr~L~V~~a~p  226 (818)
                      ..++++|||+|||.++++++|+++|++||.|..|.+.. .+|||||+|.+.++|++|++.|++..+.  |++|+|.++.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCC
Confidence            35679999999999999999999999999999998654 3899999999999999999999999999  99999999987


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      +.
T Consensus        93 ~~   94 (97)
T 1why_A           93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.48  E-value=7.5e-14  Score=128.02  Aligned_cols=81  Identities=22%  Similarity=0.471  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4456799999999999999999999999999999874     46789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      ++.++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998764

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.2e-13  Score=125.03  Aligned_cols=79  Identities=23%  Similarity=0.357  Sum_probs=72.2

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec------CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~------g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....+|||+|||.++++++|+++|++|| |..|++.      +.++|||||+|.+.++|++|+ .|++..|.|+.|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3457999999999999999999999999 9999763      567899999999999999999 9999999999999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      ++++..+
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.48  E-value=1.1e-13  Score=131.80  Aligned_cols=83  Identities=28%  Similarity=0.425  Sum_probs=74.8

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      .....++|||+|||.++++++|+++|+.||.|++|++     ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3345679999999999999999999999999999976     34568999999999999999999999999999999999


Q ss_pred             ecCCCccc
Q 003463          308 PSRPGGAR  315 (818)
Q Consensus       308 ~a~~~~~r  315 (818)
                      +++++..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99987654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=6.6e-14  Score=126.14  Aligned_cols=82  Identities=22%  Similarity=0.455  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            456799999999999999999999999999999985     456789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=4.8e-14  Score=125.48  Aligned_cols=81  Identities=20%  Similarity=0.437  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE-Ee-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL-YT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v-~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      .+.++|||+|||.++++++|+++|++||.|..+ ++     +++++|||||+|.+.++|++|++.|++..+.|++|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467999999999999999999999999999877 63     456799999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876643

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.1e-13  Score=125.41  Aligned_cols=83  Identities=16%  Similarity=0.364  Sum_probs=74.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~------~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      +....+.++|||+|||.++++++|+++|++|| |..|.+.      ++++|||||+|.+.++|++|+ .|++..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34456779999999999999999999999999 9999842      678999999999999999999 899999999999


Q ss_pred             cccccCCCCCC
Q 003463          220 DIHFSIPKDNP  230 (818)
Q Consensus       220 ~V~~a~pk~~~  230 (818)
                      +|.++.++...
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999876643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=9e-14  Score=123.11  Aligned_cols=81  Identities=23%  Similarity=0.409  Sum_probs=73.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|.+.   ++||||+|.+.++|++|++.|++..+.|+.|+|.++.+
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   81 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS   81 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccC
Confidence            345678999999999999999999999999999999874   56999999999999999999999999999999999987


Q ss_pred             CCCC
Q 003463          227 KDNP  230 (818)
Q Consensus       227 k~~~  230 (818)
                      +...
T Consensus        82 ~~~~   85 (92)
T 2dgt_A           82 RLRT   85 (92)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            6543

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.48  E-value=8.9e-14  Score=127.52  Aligned_cols=80  Identities=28%  Similarity=0.398  Sum_probs=73.0

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      .....+|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|+|..+.|++|+|++
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999875     345689999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003463          309 SRPGG  313 (818)
Q Consensus       309 a~~~~  313 (818)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98764

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.48  E-value=7.3e-14  Score=124.05  Aligned_cols=77  Identities=21%  Similarity=0.269  Sum_probs=70.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...++|||+|||+.+++++|+++|++||.|..|++.    +.++|||||+|.+.++|.+|++.|||..+.|++|+|++++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            356799999999999999999999999999999763    3457899999999999999999999999999999999987


Q ss_pred             C
Q 003463          311 P  311 (818)
Q Consensus       311 ~  311 (818)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=5.5e-14  Score=126.63  Aligned_cols=82  Identities=26%  Similarity=0.461  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            356899999999999999999999999999999984     356899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876644

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=9.7e-14  Score=126.92  Aligned_cols=79  Identities=23%  Similarity=0.366  Sum_probs=73.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCccc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r  315 (818)
                      ..++|||+|||..+++++|+++|++||.|..|++... +|||||+|.+.++|.+|++.|+|..+.|++|+|.|++++...
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            4579999999999999999999999999999998654 899999999999999999999999999999999999887643

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.48  E-value=1.1e-13  Score=131.05  Aligned_cols=79  Identities=27%  Similarity=0.435  Sum_probs=73.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++..+|||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34579999999999999999999999999999976     3567899999999999999999999999999999999999


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      +++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8765

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.48  E-value=9.1e-14  Score=126.10  Aligned_cols=83  Identities=24%  Similarity=0.475  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccc---cccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL---RRRK  218 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l---~gr~  218 (818)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+   .+++
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            34567899999999999999999999999999999984     466899999999999999999999999988   8999


Q ss_pred             ccccccCCCCC
Q 003463          219 LDIHFSIPKDN  229 (818)
Q Consensus       219 L~V~~a~pk~~  229 (818)
                      |+|.++.++..
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999987654

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.48  E-value=1.3e-13  Score=123.96  Aligned_cols=76  Identities=29%  Similarity=0.410  Sum_probs=71.1

Q ss_pred             CCccceeeecCCC-CCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          235 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       235 ~~~~tL~V~NLp~-~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...++|||+|||. .+++++|+++|++||.|..|++.   +|||||+|.+.++|.+|++.|||..+.|++|+|++++++.
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            3567999999998 99999999999999999999984   8999999999999999999999999999999999998754

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.48  E-value=5.2e-14  Score=126.70  Aligned_cols=76  Identities=14%  Similarity=0.242  Sum_probs=71.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||.++++++|+++|++||.|.++++. .++|||||+|.+.++|.+|+..|||..+.|++|+|+|++++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            35789999999999999999999999999999986 67899999999999999999999999999999999999864

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.48  E-value=1.2e-13  Score=125.07  Aligned_cols=78  Identities=26%  Similarity=0.492  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCccc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r  315 (818)
                      ..++|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..|.|+.|+|++++++..+
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            45789999999999999999999999999999986   679999999999999999999999999999999999987654


Q ss_pred             c
Q 003463          316 R  316 (818)
Q Consensus       316 ~  316 (818)
                      .
T Consensus        87 ~   87 (103)
T 2dgu_A           87 R   87 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2e-13  Score=122.46  Aligned_cols=77  Identities=27%  Similarity=0.376  Sum_probs=71.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhcc--CCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~f--G~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ...++|||+|||..+|+++|+++|++|  |.|..|++.   ++||||+|.+.++|.+|++.|||..+.|++|+|++++++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            356799999999999999999999999  999999874   789999999999999999999999999999999999886


Q ss_pred             cc
Q 003463          313 GA  314 (818)
Q Consensus       313 ~~  314 (818)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpd_A           90 DK   91 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=1e-13  Score=122.93  Aligned_cols=77  Identities=25%  Similarity=0.466  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            456789999999999999999999999999999985     356789999999999999999999999999999999998


Q ss_pred             cC
Q 003463          224 SI  225 (818)
Q Consensus       224 a~  225 (818)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=7.9e-14  Score=123.70  Aligned_cols=79  Identities=20%  Similarity=0.378  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..+.|++|+|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999884     36789999999999999999999999999999999999


Q ss_pred             ccCC
Q 003463          223 FSIP  226 (818)
Q Consensus       223 ~a~p  226 (818)
                      ++.+
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9863

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=1e-13  Score=124.38  Aligned_cols=78  Identities=24%  Similarity=0.412  Sum_probs=72.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...++|||+|||..+|+++|+++|++||.|..|++. ..++||||+|.+.++|++|++.|+|..+.|++|+|++++++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            355799999999999999999999999999999886 458999999999999999999999999999999999998865

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.48  E-value=8e-14  Score=123.80  Aligned_cols=80  Identities=24%  Similarity=0.348  Sum_probs=72.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      +....+.++|||+|||.++++++|+++|++||+|..|++    .++++|||||+|.+.++|++|++.|++..+.|++|+|
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            334567799999999999999999999999999999884    3567899999999999999999999999999999999


Q ss_pred             cccC
Q 003463          222 HFSI  225 (818)
Q Consensus       222 ~~a~  225 (818)
                      .++.
T Consensus        90 ~~a~   93 (95)
T 2ywk_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             EEcC
Confidence            9875

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.48  E-value=1.2e-13  Score=133.61  Aligned_cols=81  Identities=25%  Similarity=0.434  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...+.++|||+|||+++++++|+++|++||.|..|++...++|||||+|.+.++|++|++.|+|..|.|++|+|.++.++
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            34567999999999999999999999999999999987668999999999999999999999999999999999999875


Q ss_pred             C
Q 003463          228 D  228 (818)
Q Consensus       228 ~  228 (818)
                      .
T Consensus       149 ~  149 (150)
T 2i2y_A          149 K  149 (150)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=7.7e-14  Score=128.00  Aligned_cols=81  Identities=21%  Similarity=0.411  Sum_probs=73.3

Q ss_pred             CCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          232 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       232 ~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ......++|||+|||.++++++|+++|++||.|..|++.   +.++|||||+|.+.++|++|++.|+|..+.|++|+|++
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344456799999999999999999999999999999763   34589999999999999999999999999999999999


Q ss_pred             cCCC
Q 003463          309 SRPG  312 (818)
Q Consensus       309 a~~~  312 (818)
                      ++++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9875

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.1e-13  Score=120.25  Aligned_cols=76  Identities=30%  Similarity=0.464  Sum_probs=70.3

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc-CCCccCCceEEEEecC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSR  310 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L-nG~~i~Gr~L~V~~a~  310 (818)
                      ....++|||+|||..+++++|+++|++||.|..|++.. ++|||||+|.+.++|.+|++.| +|..+.|++|+|+|++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            34567999999999999999999999999999998863 5899999999999999999999 9999999999999985

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.47  E-value=3.6e-14  Score=127.60  Aligned_cols=78  Identities=17%  Similarity=0.361  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCC--EEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCc----ccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGD--IRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNK----PLRRR  217 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~--I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~----~l~gr  217 (818)
                      +..-.||||+|||+++|+++|+++|++||.  |.+|+     .+++++|||||+|.+.++|++|++.|++.    .|.|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            345689999999999999999999999995  45665     25789999999999999999999999997    48899


Q ss_pred             cccccccCC
Q 003463          218 KLDIHFSIP  226 (818)
Q Consensus       218 ~L~V~~a~p  226 (818)
                      +|.|.|++.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999863

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.47  E-value=7.4e-14  Score=132.52  Aligned_cols=77  Identities=23%  Similarity=0.292  Sum_probs=71.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCce-EEEEEcCHHHHHHHHHHcCCCccCC--ceEEEEecCCCcc
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-KFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGGA  314 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~-aFVeF~d~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~~~~  314 (818)
                      -.|||+||++.+|+++|+++|++||.|.+|++..+.+|+ |||+|.+.++|.+|++.|||..|.|  ++|+|+|++++.-
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            468899999999999999999999999999886666787 9999999999999999999999998  9999999998753

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.47  E-value=1e-13  Score=127.42  Aligned_cols=80  Identities=13%  Similarity=0.303  Sum_probs=72.3

Q ss_pred             CCCccceeeecCCCCCCHHHHH---HHhhccCCeEEEEecC--------CCCceEEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLR---QIFGAYGEVKEIRETP--------HKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~---~lFs~fG~I~~vr~~g--------~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      .....+|||+|||+++++++|+   ++|++||.|..|++..        .++|||||+|.+.++|++|++.|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456799999999999999999   9999999999997632        3458999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 003463          303 RIKLEPSRPGG  313 (818)
Q Consensus       303 ~L~V~~a~~~~  313 (818)
                      +|+|++++++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998765

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=1.2e-13  Score=130.79  Aligned_cols=80  Identities=16%  Similarity=0.321  Sum_probs=72.5

Q ss_pred             CccceeeecCCCCCCHHHHH----HHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~----~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...+|||+|||+.+++++|+    ++|++||.|.+|.+  ++.++|||||+|.+.++|.+|++.|||..|.|++|+|.|+
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a  107 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS  107 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEc
Confidence            45689999999999999876    69999999999876  4578999999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++...
T Consensus       108 ~~~~~~  113 (127)
T 2a3j_A          108 ETPQSQ  113 (127)
T ss_dssp             CCCCHH
T ss_pred             cCcchh
Confidence            987643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.47  E-value=5.2e-14  Score=125.41  Aligned_cols=82  Identities=22%  Similarity=0.376  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..+..+++++|||||+|.+.++|++|++.|++..|.|+.|.|.++.++
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            34567999999999999999999999999999888778889999999999999999999999999999999999999876


Q ss_pred             CC
Q 003463          228 DN  229 (818)
Q Consensus       228 ~~  229 (818)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.47  E-value=1.6e-13  Score=125.54  Aligned_cols=77  Identities=21%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCC-----ceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-----KRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G-----r~L~V~~a~  310 (818)
                      ...+|||+|||+++|+++|+++|++||.|..|++...  +||||+|.+.++|++||+.|||..|.|     +.|+|++++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~   91 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   91 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCC
Confidence            4579999999999999999999999999999998644  999999999999999999999999999     999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ++..
T Consensus        92 ~~~~   95 (108)
T 1x4c_A           92 PRSP   95 (108)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=9.3e-14  Score=125.59  Aligned_cols=81  Identities=22%  Similarity=0.295  Sum_probs=73.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhc-cCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCc-cCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGA-YGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSD-IAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~-fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~-i~Gr~L~V~~a  309 (818)
                      ...+|||+|||.++|+++|+++|++ ||.|..|++    ++.++|||||+|.+.++|.+|++.|+|.. +.|++|+|+++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a   87 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVA   87 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEc
Confidence            4579999999999999999999999 999999976    45578999999999999999999999999 99999999999


Q ss_pred             CCCcccc
Q 003463          310 RPGGARR  316 (818)
Q Consensus       310 ~~~~~r~  316 (818)
                      +++..++
T Consensus        88 ~~~~~~~   94 (104)
T 2dhg_A           88 IPKASRV   94 (104)
T ss_dssp             CCCCSCC
T ss_pred             cCCCcCC
Confidence            8876543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.47  E-value=1.1e-13  Score=128.05  Aligned_cols=77  Identities=21%  Similarity=0.397  Sum_probs=70.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..+.|++|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3455799999999999999999999999999999763     45689999999999999999999999999999999999


Q ss_pred             cC
Q 003463          309 SR  310 (818)
Q Consensus       309 a~  310 (818)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            75

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.47  E-value=1.2e-13  Score=129.40  Aligned_cols=81  Identities=26%  Similarity=0.407  Sum_probs=73.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||..+|+++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            34579999999999999999999999999999976     4556899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.47  E-value=1.2e-13  Score=130.93  Aligned_cols=82  Identities=24%  Similarity=0.448  Sum_probs=75.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++.+|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999984     4678999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 003463          222 HFSIPKD  228 (818)
Q Consensus       222 ~~a~pk~  228 (818)
                      .++.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1e-13  Score=124.21  Aligned_cols=80  Identities=11%  Similarity=0.352  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEE-EEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccc----
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIR-TLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK----  218 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~-~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~----  218 (818)
                      ..++++|||+|||.++++++|+++|++||.|. .|++     +++++|||||+|.+.++|++|++.|++..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45689999999999999999999999999998 8873     5678899999999999999999999999999999    


Q ss_pred             ccccccCCCC
Q 003463          219 LDIHFSIPKD  228 (818)
Q Consensus       219 L~V~~a~pk~  228 (818)
                      |+|.++.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999998654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=123.53  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=69.5

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEE--------EEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  301 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~--------vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G  301 (818)
                      ....+|||+|||.++++++|+++|++||.|..        +++     ++.++|||||+|.+.++|.+|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            35679999999999999999999999999998        764     35568999999999999999999999999999


Q ss_pred             ceEEEEecC
Q 003463          302 KRIKLEPSR  310 (818)
Q Consensus       302 r~L~V~~a~  310 (818)
                      ++|+|++|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999974

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=1.2e-13  Score=123.95  Aligned_cols=80  Identities=30%  Similarity=0.523  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++. +.+|||||+|.+.++|++|++.|++..|.|++|+|.++.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            3567899999999999999999999999999999864 468999999999999999999999999999999999998765


Q ss_pred             C
Q 003463          229 N  229 (818)
Q Consensus       229 ~  229 (818)
                      .
T Consensus        91 ~   91 (99)
T 2cpj_A           91 S   91 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.46  E-value=1e-13  Score=121.03  Aligned_cols=78  Identities=12%  Similarity=0.325  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~------~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..++|||+|||.++++++|+++|++||.|..+.+.      ++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            46899999999999999999999999999999841      238999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=119.58  Aligned_cols=77  Identities=22%  Similarity=0.436  Sum_probs=70.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHh-cCcccccccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~L-ng~~l~gr~L~V~~a~  225 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++. +++|||||+|.+.++|++|++.| ++..+.|++|+|.|++
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            44567999999999999999999999999999999864 36899999999999999999998 9999999999999873

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.46  E-value=8.3e-14  Score=125.36  Aligned_cols=76  Identities=24%  Similarity=0.379  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ..++|||+|||.++++++|+++|++||.|..+++. +++|||||+|.+.++|++|++.|++..+.|+.|+|.++.++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            46899999999999999999999999999999864 67999999999999999999999999999999999998763

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.1e-13  Score=124.65  Aligned_cols=81  Identities=32%  Similarity=0.448  Sum_probs=72.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ....++|||+|||.++|+++|+++|++||.|.-++. ++..+|||||+|.+.++|++|++.|||..|.|+.|+|++++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   91 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR   91 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCC
Confidence            345679999999999999999999999999854433 5667999999999999999999999999999999999999887


Q ss_pred             cc
Q 003463          313 GA  314 (818)
Q Consensus       313 ~~  314 (818)
                      ..
T Consensus        92 ~~   93 (101)
T 2fc9_A           92 GS   93 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.46  E-value=6.3e-14  Score=126.18  Aligned_cols=77  Identities=27%  Similarity=0.400  Sum_probs=72.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      .+|||+|||.++|+++|+++|++||.|..|++...++|||||+|.+.++|++|++.|+|..+.|+.|+|++++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            37999999999999999999999999999988655789999999999999999999999999999999999988653

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=4.2e-14  Score=130.30  Aligned_cols=79  Identities=20%  Similarity=0.415  Sum_probs=72.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||..+++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|+ .|||..|.|+.|+|+++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            345799999999999999999999999999999874     567899999999999999999 99999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      +++..
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            76543

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.46  E-value=1.1e-13  Score=126.51  Aligned_cols=81  Identities=20%  Similarity=0.415  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|+|..|.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999984     46679999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      ++.++.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            997654

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.46  E-value=1.6e-13  Score=127.37  Aligned_cols=81  Identities=21%  Similarity=0.415  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+    +++++|||||+|.+.++|++|++.|++..|.|+.|+|.++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            356799999999999999999999999999999884    5678899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.4e-13  Score=126.51  Aligned_cols=82  Identities=26%  Similarity=0.365  Sum_probs=73.3

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeE--------EEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK--------EIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~--------~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      ....++|||+|||..+|+++|+++|++||.|.        .|++     ++.++|||||+|.+.++|++|++.|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34567999999999999999999999999998        4654     3566899999999999999999999999999


Q ss_pred             CceEEEEecCCCccc
Q 003463          301 GKRIKLEPSRPGGAR  315 (818)
Q Consensus       301 Gr~L~V~~a~~~~~r  315 (818)
                      |++|+|++++++..+
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999887643

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=1.2e-13  Score=127.24  Aligned_cols=76  Identities=17%  Similarity=0.267  Sum_probs=71.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||..+++++|+++|++||.|..|++. ..++||||+|.+.++|++|++.|||..+.|++|+|+|++..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            45699999999999999999999999999999985 47899999999999999999999999999999999999754

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.1e-13  Score=124.49  Aligned_cols=83  Identities=19%  Similarity=0.399  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..+. .+++++|||||+|.+.++|++|++.|++..|.|+.|+|.++.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            345789999999999999999999999999995444 2567899999999999999999999999999999999999987


Q ss_pred             CCCC
Q 003463          227 KDNP  230 (818)
Q Consensus       227 k~~~  230 (818)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2fc9_A           91 RGSP   94 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.46  E-value=3.8e-14  Score=125.27  Aligned_cols=77  Identities=17%  Similarity=0.259  Sum_probs=65.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG--~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .+|||+|||.++++++|+++|++||  .|.++++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  8888773     67889999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003463          226 PKDN  229 (818)
Q Consensus       226 pk~~  229 (818)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7643

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2.6e-13  Score=125.33  Aligned_cols=80  Identities=28%  Similarity=0.358  Sum_probs=72.3

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      .+...++|||+|||..+|+++|+++|++||.|..|++     ++.+++||||+|.+.++|++|++.|++ .|.|++|+|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            3445679999999999999999999999999999976     355789999999999999999999998 8999999999


Q ss_pred             ecCCCc
Q 003463          308 PSRPGG  313 (818)
Q Consensus       308 ~a~~~~  313 (818)
                      +++++.
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            998754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.5e-13  Score=124.47  Aligned_cols=83  Identities=23%  Similarity=0.416  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            34567899999999999999999999999999999874     467889999999999999999998 999999999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999887654

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.46  E-value=2.1e-13  Score=123.41  Aligned_cols=79  Identities=25%  Similarity=0.487  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..|.|+.|.|.++.++.
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   84 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPD   84 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCc
Confidence            3467999999999999999999999999999999864   6799999999999999999999999999999999998765


Q ss_pred             CC
Q 003463          229 NP  230 (818)
Q Consensus       229 ~~  230 (818)
                      ..
T Consensus        85 ~~   86 (103)
T 2dgu_A           85 QK   86 (103)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-13  Score=130.05  Aligned_cols=80  Identities=28%  Similarity=0.411  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr----~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ..++++|||+|||+++++++|+    ++|++||+|..|.+  +++++|||||+|.+.++|++|++.|+|..|.|++|+|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            4568999999999999999876    69999999999885  46789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      |+.++.
T Consensus       106 ~a~~~~  111 (127)
T 2a3j_A          106 FSETPQ  111 (127)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998654

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.45  E-value=1.5e-13  Score=120.33  Aligned_cols=76  Identities=28%  Similarity=0.473  Sum_probs=70.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|+ .|||..+.|++|+|++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3568999999999999999999999999999865     4566899999999999999999 899999999999999998


Q ss_pred             CC
Q 003463          311 PG  312 (818)
Q Consensus       311 ~~  312 (818)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            74

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.7e-13  Score=125.21  Aligned_cols=83  Identities=24%  Similarity=0.397  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ..+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.+++ .|.|++|.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            34567899999999999999999999999999999984     466899999999999999999999998 899999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++..+
T Consensus        91 ~~a~~~~~~   99 (116)
T 2cqd_A           91 NLAYLGAKP   99 (116)
T ss_dssp             EESTTTCCC
T ss_pred             EEcccCCCc
Confidence            999776544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.45  E-value=8.5e-14  Score=122.83  Aligned_cols=73  Identities=22%  Similarity=0.289  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.-|||+||++.+||++|+++|.+||+|.++++ ..++|||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l-~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-YLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEE-cCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4678999999999999999999999999999986 348999999999999999999999999999999999987

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.45  E-value=1.5e-13  Score=127.25  Aligned_cols=79  Identities=15%  Similarity=0.346  Sum_probs=71.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456799999999999999999999999999999985     3567999999999999999999999999999999999


Q ss_pred             cccC
Q 003463          222 HFSI  225 (818)
Q Consensus       222 ~~a~  225 (818)
                      ++++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9863

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.45  E-value=2.4e-13  Score=122.91  Aligned_cols=79  Identities=18%  Similarity=0.250  Sum_probs=71.2

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||.++++++|+++|++|| |..|++     ++.++|||||+|.+.++|++|+ .|||..|.|++|+|+++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            3567999999999999999999999997 999876     3556899999999999999999 89999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2dng_A           91 EGRKQD   96 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            887643

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.45  E-value=1.7e-13  Score=128.34  Aligned_cols=82  Identities=17%  Similarity=0.439  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++|+++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..|.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3456789999999999999999999999999999984     56779999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 003463          223 FSIPKDN  229 (818)
Q Consensus       223 ~a~pk~~  229 (818)
                      ++.++..
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9976554

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.6e-13  Score=126.23  Aligned_cols=81  Identities=28%  Similarity=0.357  Sum_probs=72.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCe----EEEE-ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV----KEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I----~~vr-~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||.++|+++|+++|++||.|    ..++ .++.++|||||+|.+.++|++|++.|+|..+.|++|+|+++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            345799999999999999999999999998    4554 36778999999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            887644

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=1.2e-13  Score=123.52  Aligned_cols=80  Identities=20%  Similarity=0.262  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ....++|||+|||.++++++|+++|++||.|....+.++++|||||+|.+.++|++|++.|++..|.|+.|+|.++.++.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            34578999999999999999999999999986322456889999999999999999999999999999999999998754

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=8.1e-14  Score=123.54  Aligned_cols=78  Identities=27%  Similarity=0.370  Sum_probs=70.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCC-eEEEEecCCCCceEEEEEcCHHHHHHHHHHcCC-CccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR-SDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~-I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG-~~i~Gr~L~V~~a~~~~  313 (818)
                      ..++|||+|||.++|+++|+++|++||. |..+.+  .+++||||+|.+.++|++|++.||| ..+.|++|+|++++++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            4578999999999999999999999999 665655  3589999999999999999999999 99999999999998876


Q ss_pred             cc
Q 003463          314 AR  315 (818)
Q Consensus       314 ~r  315 (818)
                      .+
T Consensus        85 ~~   86 (93)
T 2cqh_A           85 LR   86 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=3.6e-13  Score=123.75  Aligned_cols=80  Identities=19%  Similarity=0.234  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            456899999999999999999999999999998874    4567899999999999999999999999999999999998


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      ....
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7543

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=9e-14  Score=125.55  Aligned_cols=81  Identities=22%  Similarity=0.393  Sum_probs=73.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|++++
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            4579999999999999999999999999999875     34568999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 003463          311 PGGARR  316 (818)
Q Consensus       311 ~~~~r~  316 (818)
                      ++..+.
T Consensus        87 ~~~~~~   92 (104)
T 1p1t_A           87 SEKNKE   92 (104)
T ss_dssp             CTTHHH
T ss_pred             Cccchh
Confidence            876543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.45  E-value=4.5e-14  Score=127.54  Aligned_cols=76  Identities=20%  Similarity=0.228  Sum_probs=71.0

Q ss_pred             ccceeeecCCC------CCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC-ceE
Q 003463          237 QGTLVVFNLDP------SVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-KRI  304 (818)
Q Consensus       237 ~~tL~V~NLp~------~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G-r~L  304 (818)
                      .++|||+|||.      ++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|.+|++.|||..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            56899999999      9999999999999999999976     36789999999999999999999999999999 999


Q ss_pred             EEEecCCC
Q 003463          305 KLEPSRPG  312 (818)
Q Consensus       305 ~V~~a~~~  312 (818)
                      +|.++++.
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99999764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.45  E-value=2.4e-13  Score=122.88  Aligned_cols=82  Identities=20%  Similarity=0.403  Sum_probs=73.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+++|++|| |..|++     +++++|||||+|.+.++|++|+ .|++..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            3445789999999999999999999999997 998874     4678999999999999999999 79999999999999


Q ss_pred             cccCCCCCC
Q 003463          222 HFSIPKDNP  230 (818)
Q Consensus       222 ~~a~pk~~~  230 (818)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dng_A           88 DIAEGRKQD   96 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            999876543

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.45  E-value=2e-13  Score=132.83  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=74.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||..+|+++|+++|++||.|..|++     ++.+++||||+|.+.++|++||+.||+..|.|++|+|++++
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  117 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA  117 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4579999999999999999999999999999987     45578999999999999999999999999999999999998


Q ss_pred             CCcccc
Q 003463          311 PGGARR  316 (818)
Q Consensus       311 ~~~~r~  316 (818)
                      +...++
T Consensus       118 ~~~~~~  123 (156)
T 1h2v_Z          118 GFKEGR  123 (156)
T ss_dssp             CCCTTC
T ss_pred             CCCCcC
Confidence            865443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=2.8e-13  Score=124.51  Aligned_cols=80  Identities=19%  Similarity=0.167  Sum_probs=71.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...++|||+|||..+++++|+++|++||.|..|++    ++.+++||||+|.+.++|++|++.|||..|.|+.|+|++++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            34579999999999999999999999999999875    33457899999999999999999999999999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ....
T Consensus        93 ~~~~   96 (114)
T 2do0_A           93 RALP   96 (114)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            6543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.2e-13  Score=120.20  Aligned_cols=76  Identities=21%  Similarity=0.338  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|++..+.|+.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            46799999999999999999999999999999983     4677999999999999999999999999999999998875


Q ss_pred             C
Q 003463          225 I  225 (818)
Q Consensus       225 ~  225 (818)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.45  E-value=1.2e-13  Score=123.38  Aligned_cols=77  Identities=29%  Similarity=0.404  Sum_probs=71.2

Q ss_pred             CCccceeeecCCC-CCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          235 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       235 ~~~~tL~V~NLp~-~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...++|||+|||. .+++++|+++|++||.|..|++.   +|||||+|.+.++|.+|++.|+|..+.|++|+|++++++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            3467999999998 99999999999999999999984   7999999999999999999999999999999999998765


Q ss_pred             c
Q 003463          314 A  314 (818)
Q Consensus       314 ~  314 (818)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=2.1e-13  Score=122.81  Aligned_cols=83  Identities=23%  Similarity=0.407  Sum_probs=73.5

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEE--ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       233 ~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr--~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      .....++|||+|||.++|+++|+++|+.|+.|.-++  .++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK   90 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            445668999999999999999999999998776664  356678999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003463          311 PGGAR  315 (818)
Q Consensus       311 ~~~~r  315 (818)
                      ++..+
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87643

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.4e-13  Score=124.22  Aligned_cols=80  Identities=14%  Similarity=0.294  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      .+.++|||+|||.++++++|+++|++||.|..|++... +|||||+|.+.++|++|++.|++..|.|+.|+|.++.++..
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            45789999999999999999999999999999986443 89999999999999999999999999999999999987654


Q ss_pred             C
Q 003463          230 P  230 (818)
Q Consensus       230 ~  230 (818)
                      .
T Consensus       102 ~  102 (109)
T 1x4g_A          102 M  102 (109)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=1.2e-13  Score=123.63  Aligned_cols=78  Identities=24%  Similarity=0.370  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeE-EEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce----EE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR----IK  305 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~-~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~----L~  305 (818)
                      ..++|||+|||..+++++|+++|++||.|. .|++     ++.++|||||+|.+.++|++|++.|||..+.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            457999999999999999999999999999 8865     4556799999999999999999999999999999    99


Q ss_pred             EEecCCCc
Q 003463          306 LEPSRPGG  313 (818)
Q Consensus       306 V~~a~~~~  313 (818)
                      |.|+++..
T Consensus        88 v~~a~~~~   95 (99)
T 2div_A           88 LNYATYSG   95 (99)
T ss_dssp             EEETTCCS
T ss_pred             EeecCCCC
Confidence            99998765

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.45  E-value=1.3e-13  Score=123.37  Aligned_cols=79  Identities=20%  Similarity=0.222  Sum_probs=70.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||..+++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            3457899999999999999999999999986442     34567899999999999999999999999999999999999


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      +.+.
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            7653

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.45  E-value=3.3e-13  Score=123.36  Aligned_cols=79  Identities=14%  Similarity=0.216  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccc-----ccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR-----RKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g-----r~L~V~~  223 (818)
                      ....++|||+|||.++++++|+++|++||+|..|++...  |||||+|.+.++|++||+.|++..|.|     +.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~   89 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   89 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEe
Confidence            356789999999999999999999999999999986443  999999999999999999999999999     9999999


Q ss_pred             cCCCCC
Q 003463          224 SIPKDN  229 (818)
Q Consensus       224 a~pk~~  229 (818)
                      +.++..
T Consensus        90 a~~~~~   95 (108)
T 1x4c_A           90 DGPRSP   95 (108)
T ss_dssp             SSCCSC
T ss_pred             CCCCCC
Confidence            987654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.45  E-value=7.5e-14  Score=133.27  Aligned_cols=85  Identities=28%  Similarity=0.479  Sum_probs=76.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      +....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999999999999999999999999999984     567899999999999999999999999999999999


Q ss_pred             ccccCCCCCC
Q 003463          221 IHFSIPKDNP  230 (818)
Q Consensus       221 V~~a~pk~~~  230 (818)
                      |.++.++..+
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.45  E-value=1.3e-13  Score=122.94  Aligned_cols=79  Identities=22%  Similarity=0.431  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHH----HHhhccCCeEEEEec--CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~----~lFs~fG~I~~vr~~--g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ..++|||+|||.++++++|+    ++|++||.|..|++.  +.++|||||+|.+.++|.+|++.|||..+.|+.|+|+++
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   86 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45799999999999999999    999999999999874  356899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      +++..
T Consensus        87 ~~~~~   91 (97)
T 1nu4_A           87 KTDSD   91 (97)
T ss_dssp             SSCCT
T ss_pred             cCCCc
Confidence            98764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=2.5e-13  Score=119.71  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..+.|++|+|.++.++.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            3567899999999999999999999999999999874   5699999999999999999999999999999999998765


Q ss_pred             C
Q 003463          229 N  229 (818)
Q Consensus       229 ~  229 (818)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.44  E-value=2e-13  Score=122.56  Aligned_cols=78  Identities=23%  Similarity=0.388  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--------EEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~--------v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..        +++     +++++|||||+|.+.++|++|++.|+|..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456799999999999999999999999999988        663     467899999999999999999999999999


Q ss_pred             ccccccccccC
Q 003463          215 RRRKLDIHFSI  225 (818)
Q Consensus       215 ~gr~L~V~~a~  225 (818)
                      .|+.|+|.++.
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999873

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.44  E-value=1.5e-13  Score=122.93  Aligned_cols=79  Identities=24%  Similarity=0.394  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          149 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       149 e~~srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ..++++|||+|||. ++++++|+++|++||.|..|.+   .+|||||+|.+.++|++|++.|++..+.|++|+|.++.++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcC
Confidence            35789999999998 9999999999999999999987   4899999999999999999999999999999999999776


Q ss_pred             CCC
Q 003463          228 DNP  230 (818)
Q Consensus       228 ~~~  230 (818)
                      ..+
T Consensus        84 ~~~   86 (96)
T 2kvi_A           84 ARP   86 (96)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            543

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2.5e-13  Score=123.78  Aligned_cols=82  Identities=21%  Similarity=0.313  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEeC------CCcccEEEEEEccHHHHHHHHHHhc--Cccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYTA------CKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLD  220 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~-I~~v~~~------~ksrG~AFV~F~d~e~A~~Al~~Ln--g~~l~gr~L~  220 (818)
                      .+.++|||+|||.++++++|+++|++||. |..|.+.      ++++|||||+|.+.++|++|++.|+  +..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            46789999999999999999999999998 9999853      4789999999999999999999996  5899999999


Q ss_pred             ccccCCCCCCC
Q 003463          221 IHFSIPKDNPS  231 (818)
Q Consensus       221 V~~a~pk~~~~  231 (818)
                      |.++.++....
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99998876543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.44  E-value=1.4e-13  Score=130.29  Aligned_cols=84  Identities=19%  Similarity=0.374  Sum_probs=74.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--EEe-----CCCcccEEEEEEccHHHHHHHHHHhcCc----cc
Q 003463          146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--LYT-----ACKHRGFVMISYYDIRAARTAMRALQNK----PL  214 (818)
Q Consensus       146 ~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~--v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~----~l  214 (818)
                      +....+.++|||+|||+++|+++|+++|++||.|..  |++     +++++|||||+|.+. +|++|++.|++.    .|
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            344567899999999999999999999999999966  662     678999999999999 999999999999    99


Q ss_pred             ccccccccccCCCCCC
Q 003463          215 RRRKLDIHFSIPKDNP  230 (818)
Q Consensus       215 ~gr~L~V~~a~pk~~~  230 (818)
                      .|+.|+|.++.++...
T Consensus        96 ~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           96 DGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGCCCCCEECCCSCCC
T ss_pred             CCEEEEEEECCCCCCC
Confidence            9999999999886543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.44  E-value=2.7e-13  Score=129.17  Aligned_cols=83  Identities=23%  Similarity=0.437  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|+.||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4456799999999999999999999999999999874     46779999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 003463          223 FSIPKDNP  230 (818)
Q Consensus       223 ~a~pk~~~  230 (818)
                      ++.++...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.3e-13  Score=126.57  Aligned_cols=80  Identities=23%  Similarity=0.418  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...+.++|||+|||.++++++|+++|++||+|..|++   .++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4456799999999999999999999999999999885   3457999999999999999999999999999999999999


Q ss_pred             CCC
Q 003463          225 IPK  227 (818)
Q Consensus       225 ~pk  227 (818)
                      .++
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            765

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.44  E-value=5.9e-14  Score=126.75  Aligned_cols=78  Identities=17%  Similarity=0.267  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCC------CCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccc-c
Q 003463          150 HPSRTLFVRNINS------NVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR-R  217 (818)
Q Consensus       150 ~~srtLfV~NLP~------~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g-r  217 (818)
                      ..+++|||+|||.      ++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      9999999999999999999984     47899999999999999999999999999999 9


Q ss_pred             cccccccCCC
Q 003463          218 KLDIHFSIPK  227 (818)
Q Consensus       218 ~L~V~~a~pk  227 (818)
                      .|+|.++.++
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998654

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.44  E-value=1.1e-13  Score=128.09  Aligned_cols=77  Identities=19%  Similarity=0.201  Sum_probs=70.1

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCC--CccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG--~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||++ +++++|+++|++||.|.+|++. +.+|||||+|.+.++|.+|++.|++  ..|.|++|+|.+++.+
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccc
Confidence            4579999999998 9999999999999999999985 5689999999999999999998864  5699999999999876


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus       103 ~  103 (112)
T 1x4f_A          103 K  103 (112)
T ss_dssp             S
T ss_pred             c
Confidence            5

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2.1e-13  Score=122.06  Aligned_cols=80  Identities=15%  Similarity=0.269  Sum_probs=72.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEeC--CCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr----~lFs~fG~I~~v~~~--~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +.++|||+|||.++++++|+    ++|++||.|..|++.  ...+|||||+|.+.++|++|++.|++..+.|++|+|.++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            46899999999999999999    999999999999853  223899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .+...+
T Consensus        88 ~~~~~~   93 (96)
T 2dgx_A           88 TGASGP   93 (96)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            876543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.44  E-value=1.1e-13  Score=123.27  Aligned_cols=80  Identities=24%  Similarity=0.597  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEeC--CCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr----~lFs~fG~I~~v~~~--~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ..++++|||+|||.++++++|+    ++|++||.|..|.+.  ++++|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4578999999999999999999    999999999999853  4678999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      ++.++.
T Consensus        85 ~a~~~~   90 (97)
T 1nu4_A           85 YAKTDS   90 (97)
T ss_dssp             ECSSCC
T ss_pred             EccCCC
Confidence            998754

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.9e-13  Score=125.61  Aligned_cols=83  Identities=22%  Similarity=0.371  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEE--------EEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIR--------TLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~--------~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                      ...+.++|||+|||.++++++|+++|++||.|.        .|++     +++++|||||+|.+.++|++|++.|++..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            446789999999999999999999999999998        4663     467799999999999999999999999999


Q ss_pred             ccccccccccCCCCCC
Q 003463          215 RRRKLDIHFSIPKDNP  230 (818)
Q Consensus       215 ~gr~L~V~~a~pk~~~  230 (818)
                      .|+.|+|.++.++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.44  E-value=3.9e-14  Score=132.36  Aligned_cols=77  Identities=25%  Similarity=0.446  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|+ .|||..|.|+.|+|++++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3479999999999999999999999999999875     4567899999999999999999 799999999999999998


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=6.4e-14  Score=126.52  Aligned_cols=79  Identities=24%  Similarity=0.445  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            45689999999999999999999999999988874     5677999999999999999999999999999999999999


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .++.
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            8654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.44  E-value=2.4e-13  Score=123.70  Aligned_cols=77  Identities=14%  Similarity=0.169  Sum_probs=70.5

Q ss_pred             CccceeeecCCCCC------CHHHHHHHhhccCCeEEEEe---cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc-eEE
Q 003463          236 NQGTLVVFNLDPSV------SNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIK  305 (818)
Q Consensus       236 ~~~tL~V~NLp~~v------teedL~~lFs~fG~I~~vr~---~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr-~L~  305 (818)
                      ..++|||+|||..+      |+++|+++|++||.|..|++   ++.++|||||+|.+.++|.+|+..|||..+.|+ +|+
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~   93 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   93 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEE
Confidence            45789999999999      78999999999999999976   456789999999999999999999999999998 999


Q ss_pred             EEecCCC
Q 003463          306 LEPSRPG  312 (818)
Q Consensus       306 V~~a~~~  312 (818)
                      |.++...
T Consensus        94 V~~a~~~  100 (105)
T 2nlw_A           94 VNLFTDF  100 (105)
T ss_dssp             EECSCCC
T ss_pred             EEEcchH
Confidence            9998754

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.44  E-value=3e-13  Score=121.51  Aligned_cols=77  Identities=25%  Similarity=0.396  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          148 GEHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       148 ~e~~srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ...++++|||+|||. ++++++|+++|++||.|..+++   .+|||||+|.+.++|++|++.|+|..+.|++|+|.++.+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            345689999999998 9999999999999999999987   489999999999999999999999999999999999876


Q ss_pred             C
Q 003463          227 K  227 (818)
Q Consensus       227 k  227 (818)
                      +
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.44  E-value=1.2e-13  Score=124.59  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=69.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe------cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ...++|||+|||.++++++|+++|++|| |.+|++      ++.++|||||+|.+.++|.+|+ .|+|..+.|+.|+|++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            3557999999999999999999999999 999976      3556899999999999999999 8999999999999999


Q ss_pred             cCCCc
Q 003463          309 SRPGG  313 (818)
Q Consensus       309 a~~~~  313 (818)
                      ++++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=4.9e-13  Score=119.65  Aligned_cols=76  Identities=20%  Similarity=0.392  Sum_probs=70.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ...+|||+||  ++|+++|+++|++||.|..|++ +.++|||||+|.+.++|.+|++.|+|..+.|++|+|++++++..
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            4579999996  8999999999999999999998 46789999999999999999999999999999999999988654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=5.4e-13  Score=119.71  Aligned_cols=78  Identities=21%  Similarity=0.406  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcC--CCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQY--GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~f--G~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..+.++|||+|||.++++++|+++|++|  |.|..|++   .+|||||+|.+.++|++|++.|++..|.|++|+|.++.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   88 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE---eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            3567999999999999999999999999  99999875   478999999999999999999999999999999999987


Q ss_pred             CCC
Q 003463          227 KDN  229 (818)
Q Consensus       227 k~~  229 (818)
                      +..
T Consensus        89 ~~~   91 (99)
T 2cpd_A           89 VDK   91 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.44  E-value=9.4e-14  Score=128.63  Aligned_cols=80  Identities=16%  Similarity=0.209  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcC--cccccccccccccC
Q 003463          149 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~-vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng--~~l~gr~L~V~~a~  225 (818)
                      ..++++|||+|||++ +++++|+++|++||+|..|++ .+.+|||||+|.+.++|++|++.|++  ..|.|++|+|.++.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  100 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE  100 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECc
Confidence            457899999999998 999999999999999999986 35789999999999999999998865  56999999999997


Q ss_pred             CCCC
Q 003463          226 PKDN  229 (818)
Q Consensus       226 pk~~  229 (818)
                      .+..
T Consensus       101 ~~~~  104 (112)
T 1x4f_A          101 KYKK  104 (112)
T ss_dssp             SCSS
T ss_pred             cccc
Confidence            6554

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.44  E-value=2.6e-13  Score=123.24  Aligned_cols=76  Identities=24%  Similarity=0.365  Sum_probs=69.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....+|||+|||+.+|+++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            34579999999999999999999999999999875    34568899999999999999999999999999999999985

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.8e-13  Score=126.00  Aligned_cols=82  Identities=21%  Similarity=0.395  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCE----EEEE-eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDI----RTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I----~~v~-~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..++++|||+|||.++|+++|+++|++||.|    ..++ .+++++|||||+|.+.++|++|++.|++..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4567999999999999999999999999998    4444 4788999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +.++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876543

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.44  E-value=2.7e-13  Score=123.20  Aligned_cols=78  Identities=22%  Similarity=0.429  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..|.|+.|+|.+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3457899999999999999999999999999999874    567899999999999999999999999999999999998


Q ss_pred             cC
Q 003463          224 SI  225 (818)
Q Consensus       224 a~  225 (818)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.44  E-value=2e-13  Score=134.31  Aligned_cols=77  Identities=23%  Similarity=0.295  Sum_probs=70.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-CCCCceEEEEEcCHHHHHHHHHHcCCCccCC--ceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~~~  313 (818)
                      -.+|||+||++.+|+++|+++|++||+|++|++. ..+++||||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            3579999999999999999999999999999874 4457899999999999999999999999965  999999999875

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.44  E-value=1.7e-13  Score=125.78  Aligned_cols=79  Identities=24%  Similarity=0.494  Sum_probs=72.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..+.+.++|||+|||.++++++|+++|++||.|..|.+.   +|||||+|.+.++|++|++.|+|..+.|+.|.|.++.+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  102 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL  102 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            345678999999999999999999999999999999865   89999999999999999999999999999999999987


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      +.
T Consensus       103 ~~  104 (108)
T 2jvo_A          103 PA  104 (108)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.43  E-value=6.4e-13  Score=124.26  Aligned_cols=79  Identities=20%  Similarity=0.288  Sum_probs=72.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....+|||+|||..+++++|+++|++||.|..|++    ++.++|||||+|.+.++|.+|++.|||..+.|++|+|+++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            34579999999999999999999999999999976    34578999999999999999999999999999999999998


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      +..
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.43  E-value=3.4e-13  Score=122.75  Aligned_cols=80  Identities=14%  Similarity=0.296  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCC------cHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccc-
Q 003463          148 GEHPSRTLFVRNINSNV------EDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-  217 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~v------TEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr-  217 (818)
                      ....+++|||+|||.++      ++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|+|..|.|+ 
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            34457899999999999      78999999999999999985   567899999999999999999999999999998 


Q ss_pred             cccccccCCC
Q 003463          218 KLDIHFSIPK  227 (818)
Q Consensus       218 ~L~V~~a~pk  227 (818)
                      +|+|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998654

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.43  E-value=1.6e-13  Score=123.74  Aligned_cols=78  Identities=18%  Similarity=0.399  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ....++|||+|||.++++++|+++|++|| |..|++      +++++|||||+|.+.++|++|+ .|++..|.|+.|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            45679999999999999999999999999 999984      4667999999999999999999 799999999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      ++.++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.43  E-value=1.5e-13  Score=116.66  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=65.3

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +|||+|||+++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++ |+|..+.|++|+|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999975     45678999999999999999998 9999999999999885

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.43  E-value=2.4e-13  Score=117.56  Aligned_cols=71  Identities=15%  Similarity=0.362  Sum_probs=65.5

Q ss_pred             CcEEEEcCCCCCC------cHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccc-cccc
Q 003463          152 SRTLFVRNINSNV------EDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-KLDI  221 (818)
Q Consensus       152 srtLfV~NLP~~v------TEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr-~L~V  221 (818)
                      +++|||+|||.++      ++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|+|..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4799999999999      78999999999999999984   567899999999999999999999999999999 8887


Q ss_pred             c
Q 003463          222 H  222 (818)
Q Consensus       222 ~  222 (818)
                      .
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.43  E-value=3.4e-13  Score=123.73  Aligned_cols=81  Identities=27%  Similarity=0.401  Sum_probs=70.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....++|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.+ +..+.|+.|+|++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345679999999999999999999999999999976     3567899999999999999999976 5999999999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      +.++..+
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9887644

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=3.2e-13  Score=123.06  Aligned_cols=79  Identities=20%  Similarity=0.245  Sum_probs=72.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCC-eEEEEec------CCCCceEEEEEcCHHHHHHHHHHcC--CCccCCceEEE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRET------PHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKL  306 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~-I~~vr~~------g~srG~aFVeF~d~e~A~~Ai~~Ln--G~~i~Gr~L~V  306 (818)
                      ..++|||+|||..+|+++|+++|++||. |..|++.      +.++|||||+|.+.++|.+|++.|+  +..+.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4578999999999999999999999998 9999764      3678999999999999999999996  58999999999


Q ss_pred             EecCCCcc
Q 003463          307 EPSRPGGA  314 (818)
Q Consensus       307 ~~a~~~~~  314 (818)
                      ++++++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99988764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=2.1e-13  Score=123.66  Aligned_cols=81  Identities=32%  Similarity=0.473  Sum_probs=73.0

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....++|||+|||+.+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++. ++..|.|+.|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            445679999999999999999999999999999875     345679999999999999999998 99999999999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      ++++..+
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9887643

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=2.4e-13  Score=122.40  Aligned_cols=83  Identities=20%  Similarity=0.436  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE--eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~--~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ...+.++|||+|||.++++++|+++|+.|+.|..+.  .+++++|||||+|.+.++|++|++.|++..|.|+.|+|.++.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK   90 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            345789999999999999999999999998877776  367789999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 003463          226 PKDNP  230 (818)
Q Consensus       226 pk~~~  230 (818)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=2.7e-13  Score=123.51  Aligned_cols=77  Identities=10%  Similarity=0.185  Sum_probs=70.3

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....++|||+|||+++|+++|+++|++||.|.+|++.    +.++|||||+|.+.++|.+|+. ++|..+.|+.|+|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3456799999999999999999999999999999763    5678999999999999999999 9999999999999987


Q ss_pred             CC
Q 003463          310 RP  311 (818)
Q Consensus       310 ~~  311 (818)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=1.3e-13  Score=122.23  Aligned_cols=79  Identities=20%  Similarity=0.353  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEeCCCcccEEEEEEccHHHHHHHHHHhcC-cccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYTACKHRGFVMISYYDIRAARTAMRALQN-KPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~-I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng-~~l~gr~L~V~~a~pk  227 (818)
                      .+.++|||+|||.++++++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.|++ ..+.|++|+|.++.++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            46789999999999999999999999999 665554  4689999999999999999999999 9999999999999876


Q ss_pred             CCC
Q 003463          228 DNP  230 (818)
Q Consensus       228 ~~~  230 (818)
                      ...
T Consensus        84 ~~~   86 (93)
T 2cqh_A           84 KLR   86 (93)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=5.7e-13  Score=118.59  Aligned_cols=78  Identities=18%  Similarity=0.177  Sum_probs=70.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-ec-CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-~~-g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...+|||+|||+.+++++|+++|++||.|..|+ +. ....+.|||+|.+.++|.+|++.|||..+.|++|+|++++++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            457899999999999999999999999999995 43 3345569999999999999999999999999999999998874

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.42  E-value=2.8e-13  Score=118.69  Aligned_cols=76  Identities=24%  Similarity=0.452  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|+ .|++..+.|+.|+|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3589999999999999999999999999999873     5678999999999999999999 899999999999999987


Q ss_pred             CC
Q 003463          226 PK  227 (818)
Q Consensus       226 pk  227 (818)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.42  E-value=1.5e-13  Score=126.56  Aligned_cols=77  Identities=13%  Similarity=0.283  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...++|||+|||.++++++|+++|++||.|..|.+. +.+|||||+|.+.++|++|++.|++..+.|+.|.|.|+...
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            346899999999999999999999999999999864 58899999999999999999999999999999999998643

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=2e-13  Score=126.08  Aligned_cols=80  Identities=16%  Similarity=0.294  Sum_probs=72.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...++|||+|||..+|+++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++. ++..|.|+.|+|+++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            34579999999999999999999999999999976     345689999999999999999997 999999999999999


Q ss_pred             CCCccc
Q 003463          310 RPGGAR  315 (818)
Q Consensus       310 ~~~~~r  315 (818)
                      +++..+
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            887643

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.42  E-value=1.6e-13  Score=126.94  Aligned_cols=78  Identities=10%  Similarity=0.094  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEe-CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG-~I~~v~~-~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...++|||+|||+++++++|+++|++|| +|..+.+ ..+++|||||+|.+.++|++|++.|+|..|.|+.|+|.++...
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3468999999999999999999999999 8999986 4678999999999999999999999999999999999998643

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.42  E-value=4.8e-13  Score=130.15  Aligned_cols=81  Identities=25%  Similarity=0.410  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            346799999999999999999999999999999985     567899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003463          224 SIPKDN  229 (818)
Q Consensus       224 a~pk~~  229 (818)
                      +.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            987543

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.42  E-value=3.5e-13  Score=123.39  Aligned_cols=77  Identities=25%  Similarity=0.508  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          149 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       149 e~~srtLfV~NLP~~-vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ..+.++|||+|||.+ +++++|+++|++||.|..|.+   .+|||||+|.+.++|++|++.|++..|.|+.|+|.++.+.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            345689999999999 999999999999999999987   7899999999999999999999999999999999999754


Q ss_pred             C
Q 003463          228 D  228 (818)
Q Consensus       228 ~  228 (818)
                      .
T Consensus       101 ~  101 (110)
T 1wf1_A          101 K  101 (110)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.42  E-value=1.7e-13  Score=134.11  Aligned_cols=78  Identities=13%  Similarity=0.209  Sum_probs=71.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccC--CeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG--~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ...+|||+|||+++|+++|+++|++||  .|.+|++     ++.++|||||+|.+.++|++||..|||..|.|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            346999999999999999999999999  9999875     567789999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003463          309 SRPGG  313 (818)
Q Consensus       309 a~~~~  313 (818)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            98754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.42  E-value=4.1e-13  Score=126.60  Aligned_cols=74  Identities=26%  Similarity=0.280  Sum_probs=68.0

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCce-EEEEEcCHHHHHHHHHHcCCCccCC--ceEEEEecCCCc
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-KFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  313 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~-aFVeF~d~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~~~  313 (818)
                      .|||+||++.+|+++|+++|++||.|++|++..+ .|+ |||+|.+.++|.+|++.|||..|.|  +.|+|+||+++.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            4689999999999999999999999999987544 586 9999999999999999999999988  699999999875

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.42  E-value=1.5e-13  Score=130.05  Aligned_cols=79  Identities=23%  Similarity=0.381  Sum_probs=71.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEE--EEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCC----ccCCc
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS----DIAGK  302 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~--vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~----~i~Gr  302 (818)
                      ....++|||+|||+++|+++|+++|++||.|..  |++     ++.++|||||+|.+. +|.+|++.|||.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345679999999999999999999999999966  654     567899999999999 999999999999    99999


Q ss_pred             eEEEEecCCCc
Q 003463          303 RIKLEPSRPGG  313 (818)
Q Consensus       303 ~L~V~~a~~~~  313 (818)
                      +|+|++++++.
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.42  E-value=1.2e-13  Score=122.57  Aligned_cols=76  Identities=20%  Similarity=0.241  Sum_probs=67.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||.++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            3479999999999999999999999999875532     45678999999999999999999999999999999999986


Q ss_pred             C
Q 003463          311 P  311 (818)
Q Consensus       311 ~  311 (818)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            5

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=5.7e-13  Score=122.54  Aligned_cols=78  Identities=21%  Similarity=0.284  Sum_probs=70.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCcc--------CCc
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI--------AGK  302 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i--------~Gr  302 (818)
                      ....+|||+|||..+++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..+        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            45579999999999999999999999999999976    345689999999999999999999999999        578


Q ss_pred             eEEEEecCCC
Q 003463          303 RIKLEPSRPG  312 (818)
Q Consensus       303 ~L~V~~a~~~  312 (818)
                      +|+|.|++++
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8999999875

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.41  E-value=3.5e-13  Score=117.81  Aligned_cols=76  Identities=18%  Similarity=0.390  Sum_probs=68.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ +++..+.|+.|.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            3457899999999999999999999999999999984     47789999999999999999997 58888999999998


Q ss_pred             cc
Q 003463          223 FS  224 (818)
Q Consensus       223 ~a  224 (818)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.41  E-value=4.5e-13  Score=117.09  Aligned_cols=75  Identities=27%  Similarity=0.401  Sum_probs=67.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....++|||+|||+.+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++ +++..+.|+.|+|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            345679999999999999999999999999999976     35668999999999999999996 688899999999987


Q ss_pred             c
Q 003463          309 S  309 (818)
Q Consensus       309 a  309 (818)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=1e-12  Score=117.55  Aligned_cols=80  Identities=19%  Similarity=0.321  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...+.++|||+||  ++++++|+++|++||+|..|.+ .+++|||||+|.+.++|++|++.|++..|.|++|+|.++.++
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~   87 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            3456799999996  9999999999999999999987 578999999999999999999999999999999999999876


Q ss_pred             CCC
Q 003463          228 DNP  230 (818)
Q Consensus       228 ~~~  230 (818)
                      ...
T Consensus        88 ~~~   90 (97)
T 1x5p_A           88 PML   90 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=1.1e-13  Score=120.40  Aligned_cols=76  Identities=21%  Similarity=0.371  Sum_probs=69.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+.+++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            3568999999999999999999999999999975     35568999999999999999999999999999999988765


Q ss_pred             C
Q 003463          311 P  311 (818)
Q Consensus       311 ~  311 (818)
                      .
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.41  E-value=2.5e-13  Score=119.48  Aligned_cols=76  Identities=13%  Similarity=0.302  Sum_probs=70.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...+|||+|||+++++++|+++|++| .|..+++. .++|||||+|.+.++|++|++.|||..+.|++|+|+++..+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            35689999999999999999999999 99999885 788999999999999999999999999999999999987643

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.41  E-value=1.1e-13  Score=121.83  Aligned_cols=75  Identities=21%  Similarity=0.439  Sum_probs=67.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEec-----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ++|||+|||.++++++|+++|++||.|.+|++.     +.++|||||+|.+.+ |.+|+..|||..+.|++|+|++|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            479999999999999999999999999999763     567899999999999 99999999999999999999999875


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.41  E-value=2e-13  Score=118.13  Aligned_cols=69  Identities=16%  Similarity=0.247  Sum_probs=63.8

Q ss_pred             cceeeecCCCCC------CHHHHHHHhhccCCeEEEEe---cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc-eEEE
Q 003463          238 GTLVVFNLDPSV------SNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIKL  306 (818)
Q Consensus       238 ~tL~V~NLp~~v------teedL~~lFs~fG~I~~vr~---~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr-~L~V  306 (818)
                      ++|||+|||..+      ++++|+++|++||.|.+|++   ++.++|||||+|.+.++|.+|++.|||..+.|+ +|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            589999999999      77999999999999999976   446789999999999999999999999999999 8876

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=6.9e-13  Score=121.96  Aligned_cols=79  Identities=16%  Similarity=0.322  Sum_probs=70.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccc--------cc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPL--------RR  216 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l--------~g  216 (818)
                      +.+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            456789999999999999999999999999999874    467899999999999999999999999999        46


Q ss_pred             ccccccccCCC
Q 003463          217 RKLDIHFSIPK  227 (818)
Q Consensus       217 r~L~V~~a~pk  227 (818)
                      ++|.|.|+.|+
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            77888888754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.40  E-value=2.7e-13  Score=132.78  Aligned_cols=77  Identities=16%  Similarity=0.252  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG--~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..++|||+|||+++|+++|+++|++||  .|..|++     +++++|||||+|.+.++|++||+.|+|..|.|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  9999884     678899999999999999999999999999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8653

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.40  E-value=1.9e-13  Score=122.95  Aligned_cols=79  Identities=23%  Similarity=0.328  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEE----EecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v----r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...+|||+|||.++|+++|+++|++||.|..+    +.++.++|||||+|.+.++|++|++ |||..+.|+.|+|.++++
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~   94 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   94 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCC
Confidence            45799999999999999999999999987652    2356789999999999999999998 999999999999999998


Q ss_pred             Cccc
Q 003463          312 GGAR  315 (818)
Q Consensus       312 ~~~r  315 (818)
                      +..+
T Consensus        95 ~~~~   98 (101)
T 1fj7_A           95 RDGT   98 (101)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.40  E-value=2.1e-13  Score=121.94  Aligned_cols=79  Identities=19%  Similarity=0.240  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ....++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|++..|.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34568999999999999999999999999886432     3567899999999999999999999999999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=5.5e-13  Score=117.63  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=70.2

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....+|||+|||.++++++|+++|++| .|..|++    ++.++|||||+|.+.++|.+|++ |||..|.|+.|+|.+++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECC
Confidence            356799999999999999999999999 8988875    45568899999999999999999 99999999999999998


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.40  E-value=9e-13  Score=125.13  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=69.4

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ....++|||+|||..+++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345679999999999999999999999999999976     355789999999999999999999999999999999998


Q ss_pred             c
Q 003463          309 S  309 (818)
Q Consensus       309 a  309 (818)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.40  E-value=1.4e-13  Score=122.26  Aligned_cols=76  Identities=20%  Similarity=0.232  Sum_probs=67.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|++..|.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            3568999999999999999999999999986443     25678999999999999999999999999999999999987


Q ss_pred             C
Q 003463          225 I  225 (818)
Q Consensus       225 ~  225 (818)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=1e-12  Score=118.59  Aligned_cols=81  Identities=15%  Similarity=0.318  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++  ++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            3456789999999999999999999999999999874     47789999999999999999999  4778999999999


Q ss_pred             ccCCCCCC
Q 003463          223 FSIPKDNP  230 (818)
Q Consensus       223 ~a~pk~~~  230 (818)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99887654

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=7.8e-13  Score=120.13  Aligned_cols=79  Identities=11%  Similarity=0.196  Sum_probs=71.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE-EEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~-v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ....++|||+|||+++|+++|+++|++||.|.. |.+    +++++|||||+|.+.++|++|++. ++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            346789999999999999999999999999987 653    678899999999999999999997 99999999999998


Q ss_pred             cCCCC
Q 003463          224 SIPKD  228 (818)
Q Consensus       224 a~pk~  228 (818)
                      +.+++
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=3.8e-13  Score=122.56  Aligned_cols=77  Identities=12%  Similarity=0.314  Sum_probs=70.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +.+.++|||+|||.++|+++|+++|++||+|..|.+    .++++|||||+|.+.++|++|+. +++..+.|+.|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999984    36789999999999999999999 8999999999999876


Q ss_pred             CC
Q 003463          225 IP  226 (818)
Q Consensus       225 ~p  226 (818)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.39  E-value=5.3e-13  Score=122.48  Aligned_cols=81  Identities=16%  Similarity=0.401  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.+ +..+.|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999985     3678999999999999999999976 599999999999


Q ss_pred             ccCCCCC
Q 003463          223 FSIPKDN  229 (818)
Q Consensus       223 ~a~pk~~  229 (818)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.39  E-value=6e-13  Score=117.41  Aligned_cols=78  Identities=9%  Similarity=0.215  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....++|||+|||.++++++|+++|+.| .|..|++    +++++|||||+|.+.++|++|++ |++..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            4567899999999999999999999999 8888873    56789999999999999999999 9999999999999998


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.3e-12  Score=117.92  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=70.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      .....+|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++  ++..+.|++|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            345679999999999999999999999999999975     35668999999999999999999  57899999999999


Q ss_pred             cCCCcc
Q 003463          309 SRPGGA  314 (818)
Q Consensus       309 a~~~~~  314 (818)
                      ++++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            988654

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.39  E-value=3.9e-13  Score=123.57  Aligned_cols=80  Identities=18%  Similarity=0.283  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH---HHhhcCCCEEEEEeC--------CCcccEEEEEEccHHHHHHHHHHhcCcccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELR---ALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRR  217 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr---~lFs~fG~I~~v~~~--------~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr  217 (818)
                      ....++|||+|||+++++++|+   ++|++||+|..|++.        ++++|||||+|.+.++|++|++.|++..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3457899999999999999999   999999999999842        24569999999999999999999999999999


Q ss_pred             cccccccCCCC
Q 003463          218 KLDIHFSIPKD  228 (818)
Q Consensus       218 ~L~V~~a~pk~  228 (818)
                      +|+|.++.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998765

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.39  E-value=6.8e-13  Score=124.07  Aligned_cols=82  Identities=22%  Similarity=0.422  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3456789999999999999999999999999999874    456899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003463          224 SIPKDN  229 (818)
Q Consensus       224 a~pk~~  229 (818)
                      +.+...
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            987554

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.3e-12  Score=118.76  Aligned_cols=78  Identities=23%  Similarity=0.293  Sum_probs=70.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEE-EEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~-vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||+++|+++|+++|++||.|.. |++    +++++|||||+|.+.++|++||+. ++..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            34579999999999999999999999999987 765    567799999999999999999997 999999999999998


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      .++.
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7644

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.39  E-value=8.1e-13  Score=125.39  Aligned_cols=78  Identities=23%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccE-EEEEEccHHHHHHHHHHhcCccccc--ccccccccCCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDN  229 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~-AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~a~pk~~  229 (818)
                      -.|||+||++.+|+++|+++|++||+|.+|++..+.+|| |||+|.+.++|++|++.|+|..|.|  +.|+|+|++++..
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            467799999999999999999999999999876667888 9999999999999999999999988  8999999988754


Q ss_pred             C
Q 003463          230 P  230 (818)
Q Consensus       230 ~  230 (818)
                      .
T Consensus       109 ~  109 (130)
T 3zzy_A          109 N  109 (130)
T ss_dssp             C
T ss_pred             e
Confidence            3

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.39  E-value=7.3e-13  Score=125.75  Aligned_cols=77  Identities=26%  Similarity=0.490  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456899999999999999999999999999999984     45689999999999999999999999999999999998


Q ss_pred             cc
Q 003463          223 FS  224 (818)
Q Consensus       223 ~a  224 (818)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.39  E-value=9.9e-13  Score=117.22  Aligned_cols=72  Identities=26%  Similarity=0.383  Sum_probs=65.0

Q ss_pred             cceeeecCCCCCCHHH----HHHHhhcc-CCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          238 GTLVVFNLDPSVSNED----LRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       238 ~tL~V~NLp~~vteed----L~~lFs~f-G~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..|||.|||..+++++    |+++|++| |+|.+|  ++   |+|||+|.+.++|.+|++.|+|..+.||+|+|.||+.+
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~   84 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKN   84 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCS
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCC
Confidence            3499999999999988    55899999 599998  33   99999999999999999999999999999999999876


Q ss_pred             cc
Q 003463          313 GA  314 (818)
Q Consensus       313 ~~  314 (818)
                      ..
T Consensus        85 sd   86 (96)
T 2diu_A           85 RE   86 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.38  E-value=1.8e-13  Score=120.39  Aligned_cols=76  Identities=21%  Similarity=0.414  Sum_probs=67.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.+ |++|++.|++..+.|++|+|.++.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999884     3678999999999999 99999999999999999999999875


Q ss_pred             CC
Q 003463          228 DN  229 (818)
Q Consensus       228 ~~  229 (818)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.38  E-value=3.3e-13  Score=118.68  Aligned_cols=76  Identities=16%  Similarity=0.371  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...++|||+|||+++++++|+++|++| .|..+++. +++|||||+|.+.++|++|++.|++..+.|++|+|.++..+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            457899999999999999999999999 99998874 78999999999999999999999999999999999998643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.38  E-value=3.5e-13  Score=114.79  Aligned_cols=71  Identities=27%  Similarity=0.417  Sum_probs=65.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ++|||+|||.++++++|+++|++||.|..+++     ++.++|+|||+|.+.++|++|++.++ ..+.|++|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            37999999999999999999999999998875     35568999999999999999999999 9999999999986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=1.3e-12  Score=116.29  Aligned_cols=79  Identities=23%  Similarity=0.296  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE--eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~--~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...++|||+|||+++++++|+++|++||.|..|+  ...+..|.|||+|.+.++|++|++.|++..|.|++|+|.++.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            3468999999999999999999999999999994  34445666999999999999999999999999999999999876


Q ss_pred             C
Q 003463          228 D  228 (818)
Q Consensus       228 ~  228 (818)
                      .
T Consensus        93 ~   93 (96)
T 2e44_A           93 M   93 (96)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.38  E-value=3.3e-13  Score=114.57  Aligned_cols=70  Identities=16%  Similarity=0.401  Sum_probs=65.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++ +++..+.|++|.|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999874     56789999999999999999998 9999999999999875

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=8.5e-13  Score=122.49  Aligned_cols=78  Identities=17%  Similarity=0.313  Sum_probs=70.2

Q ss_pred             CCCCCcEEEE--cCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccc-----cccccc
Q 003463          148 GEHPSRTLFV--RNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-----RRRKLD  220 (818)
Q Consensus       148 ~e~~srtLfV--~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l-----~gr~L~  220 (818)
                      ...++++|||  +||+.++++++|+++|++||+|..|.+. ..+|||||+|.+.++|++|++.|+|..+     .+++|+
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~   99 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            3457899999  7799999999999999999999999864 4689999999999999999999999988     689999


Q ss_pred             ccccCC
Q 003463          221 IHFSIP  226 (818)
Q Consensus       221 V~~a~p  226 (818)
                      |.|+..
T Consensus       100 v~~a~~  105 (114)
T 2cq2_A          100 LNFVEK  105 (114)
T ss_dssp             EEEESC
T ss_pred             EEeccc
Confidence            998764

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=3.2e-13  Score=124.30  Aligned_cols=77  Identities=17%  Similarity=0.381  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC-----CCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~-----~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...++|||+|||.++++++|+++|++||.|..|++.     ++++|||||+|.+.++|++|+ .|++..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            346899999999999999999999999999999853     678999999999999999999 89999999999999998


Q ss_pred             CCC
Q 003463          225 IPK  227 (818)
Q Consensus       225 ~pk  227 (818)
                      .++
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=1.3e-12  Score=116.41  Aligned_cols=76  Identities=17%  Similarity=0.330  Sum_probs=67.6

Q ss_pred             CCCcE-EEEcCCCCCCcHHH----HHHHhhcC-CCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          150 HPSRT-LFVRNINSNVEDSE----LRALFEQY-GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       150 ~~srt-LfV~NLP~~vTEee----Lr~lFs~f-G~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      .|+.| |||+|||.++++++    |+++|++| |+|.+|  ++   |+|||.|.+.++|++|++.|+|..+.||+|+|.|
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            35666 99999999999988    55899999 599998  33   9999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003463          224 SIPKDNP  230 (818)
Q Consensus       224 a~pk~~~  230 (818)
                      +..+.+.
T Consensus        81 A~~~sd~   87 (96)
T 2diu_A           81 TPKNREL   87 (96)
T ss_dssp             SCCSCCC
T ss_pred             cCCCcce
Confidence            9876643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=2.9e-12  Score=113.91  Aligned_cols=79  Identities=16%  Similarity=0.301  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      ...++|||+|||.++++++|+++|++||.|..|........||||+|.+.++|++|++ |++..|.|+.|.|.++.++..
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            4568999999999999999999999999999985433222299999999999999999 999999999999999876554

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.37  E-value=4e-13  Score=120.87  Aligned_cols=80  Identities=16%  Similarity=0.230  Sum_probs=70.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..+.    .+++++|||||+|.+.++|++|++ |++..|.|+.|+|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            34678999999999999999999999999765511    356789999999999999999999 9999999999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87653

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.37  E-value=1.4e-12  Score=115.47  Aligned_cols=77  Identities=25%  Similarity=0.401  Sum_probs=63.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCc--cCCceEEEEecCCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSRPG  312 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~--i~Gr~L~V~~a~~~  312 (818)
                      ....+|||+|||+++|+++|+++|++||.|.+|++...++|||||+|.+.++|++    |++..  +.|++|.|.+++++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            3457999999999999999999999999999999877789999999999999983    56655  45999999999987


Q ss_pred             ccc
Q 003463          313 GAR  315 (818)
Q Consensus       313 ~~r  315 (818)
                      ..+
T Consensus        85 ~~~   87 (89)
T 3d2w_A           85 HNK   87 (89)
T ss_dssp             ---
T ss_pred             CcC
Confidence            643

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.37  E-value=1.5e-12  Score=128.12  Aligned_cols=79  Identities=20%  Similarity=0.244  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC-CCcccEEEEEEccHHHHHHHHHHhcCccccc--ccccccccCCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-CKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKD  228 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~-~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~a~pk~  228 (818)
                      ..+|||+||++++|+++|+++|++||+|++|++. .+.+|||||+|.+.++|++|++.|+|..|.|  ++|+|.|++++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            4578999999999999999999999999999863 4468899999999999999999999999965  999999999875


Q ss_pred             CC
Q 003463          229 NP  230 (818)
Q Consensus       229 ~~  230 (818)
                      ..
T Consensus       126 l~  127 (164)
T 1sjr_A          126 LN  127 (164)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=1.4e-12  Score=115.98  Aligned_cols=77  Identities=23%  Similarity=0.372  Sum_probs=67.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...+|||+|||.++|+++|+++|++||.|.+|........||||+|.+.++|.+|+. |+|..|.|+.|+|+++.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            456899999999999999999999999999984433222299999999999999999 99999999999999987654

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.37  E-value=1.1e-12  Score=121.50  Aligned_cols=75  Identities=21%  Similarity=0.294  Sum_probs=65.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce-----EEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-----IKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~-----L~V~~a~  310 (818)
                      ...+|||.|||+++|+++|+++|++||.|..|++...  |||||+|.+.++|++||+.|||.+|.|++     |+|..+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            3568999999999999999999999999999998644  99999999999999999999999999998     6666665


Q ss_pred             CC
Q 003463          311 PG  312 (818)
Q Consensus       311 ~~  312 (818)
                      +.
T Consensus        93 ~~   94 (115)
T 3beg_B           93 PR   94 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=1.2e-12  Score=121.58  Aligned_cols=76  Identities=18%  Similarity=0.215  Sum_probs=68.9

Q ss_pred             Cccceee--ecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCcc-----CCceEEEEe
Q 003463          236 NQGTLVV--FNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-----AGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V--~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i-----~Gr~L~V~~  308 (818)
                      ...+|||  +||+..+++++|+++|++||.|.+|.+. ..+|||||+|.+.++|++|++.|||+++     .|++|.|.|
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            3568999  6699999999999999999999999885 3589999999999999999999999988     689999999


Q ss_pred             cCCC
Q 003463          309 SRPG  312 (818)
Q Consensus       309 a~~~  312 (818)
                      ++.-
T Consensus       103 a~~~  106 (114)
T 2cq2_A          103 VEKV  106 (114)
T ss_dssp             ESCC
T ss_pred             cccC
Confidence            8754

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.36  E-value=1.3e-12  Score=121.91  Aligned_cols=77  Identities=18%  Similarity=0.371  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .|++..|.|+.|+|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999999999874     5778999999999999999999 799999999999999987


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.36  E-value=3.2e-13  Score=115.01  Aligned_cols=71  Identities=17%  Similarity=0.430  Sum_probs=66.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ++|||+|||.++++++|+++|++||+|..+.+     +++++|||||+|.+.++|++|++.++ ..+.|++|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            57999999999999999999999999988873     46789999999999999999999988 9999999999876

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=9.5e-13  Score=121.53  Aligned_cols=80  Identities=19%  Similarity=0.437  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|.|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            34589999999999999999999999999998874     367899999999999999999997 999999999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .++...
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            887653

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.35  E-value=1.4e-12  Score=128.29  Aligned_cols=83  Identities=19%  Similarity=0.395  Sum_probs=74.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          147 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       147 ~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....+.++|||+|||.++++++|+.+|++||.|..|.+     +++++|||||+|.+.++|++||+.|++..|.|+.|.|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  146 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  146 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999884     5667999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 003463          222 HFSIPKDN  229 (818)
Q Consensus       222 ~~a~pk~~  229 (818)
                      .|+.++..
T Consensus       147 ~~a~~~~~  154 (165)
T 1rk8_A          147 DWCFVKGP  154 (165)
T ss_dssp             EESEECC-
T ss_pred             EEecCCCC
Confidence            99976553

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.35  E-value=1.4e-12  Score=124.88  Aligned_cols=80  Identities=28%  Similarity=0.380  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEE--------E--EecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------I--RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~--------v--r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      ...+|||+|||+.+|+++|+++|++||.|..        +  ..++.++|||||+|.+.++|.+|+..|||..|.|+.|+
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~  123 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV  123 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4578999999999999999999999998865        3  34678899999999999999999999999999999999


Q ss_pred             EEecCCCccc
Q 003463          306 LEPSRPGGAR  315 (818)
Q Consensus       306 V~~a~~~~~r  315 (818)
                      |.++++...+
T Consensus       124 V~~a~~~~~~  133 (143)
T 3egn_A          124 VQFARSARPK  133 (143)
T ss_dssp             EEECCCSCC-
T ss_pred             EEECCCCCCc
Confidence            9999876543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=5.7e-13  Score=123.07  Aligned_cols=78  Identities=10%  Similarity=0.112  Sum_probs=70.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCe-EEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-KEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I-~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ....+|||+|||+++|+++|+++|++||.| ..|++    ++.++|||||+|.+.++|++||+. |+..|.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            345799999999999999999999999999 66655    466799999999999999999986 999999999999999


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      .++.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.35  E-value=1.4e-12  Score=124.95  Aligned_cols=81  Identities=19%  Similarity=0.401  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--------E--EeCCCcccEEEEEEccHHHHHHHHHHhcCccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------L--YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  218 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~--------v--~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~  218 (818)
                      ..++++|||+|||.++|+++|+++|++||.|..        +  ..+++++|||||+|.+.++|++|++.|+|..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            356799999999999999999999999998754        2  246889999999999999999999999999999999


Q ss_pred             ccccccCCCCC
Q 003463          219 LDIHFSIPKDN  229 (818)
Q Consensus       219 L~V~~a~pk~~  229 (818)
                      |.|.++.+...
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999976543

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.34  E-value=5.8e-13  Score=127.56  Aligned_cols=77  Identities=17%  Similarity=0.146  Sum_probs=69.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCC---eEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~---I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ...+|||+|||+++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++||+ ||+..|.|+.|+|.+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~  121 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFK  121 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            4568999999999999999999999999   777754    35678999999999999999999 999999999999999


Q ss_pred             cCCCc
Q 003463          309 SRPGG  313 (818)
Q Consensus       309 a~~~~  313 (818)
                      +.++.
T Consensus       122 a~~~e  126 (136)
T 2hgl_A          122 SHRTE  126 (136)
T ss_dssp             CCHHH
T ss_pred             CChHH
Confidence            86543

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.34  E-value=1.9e-12  Score=114.51  Aligned_cols=76  Identities=22%  Similarity=0.470  Sum_probs=63.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcc--cccccccccccCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSIP  226 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~--l~gr~L~V~~a~p  226 (818)
                      ..+..+|||+|||+++|+++|+++|++||.|.+|++...++|||||+|.+.++|++    +++..  +.|+.|.|.++.+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~   83 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEP   83 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCC
Confidence            35678999999999999999999999999999999877799999999999999984    34544  4589999999987


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      +.
T Consensus        84 k~   85 (89)
T 3d2w_A           84 KH   85 (89)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.34  E-value=7.3e-13  Score=112.33  Aligned_cols=70  Identities=23%  Similarity=0.453  Sum_probs=64.6

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++ +++..+.|++|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            5899999999999999999999999999975     35678999999999999999998 5999999999999875

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=1.8e-12  Score=117.64  Aligned_cols=78  Identities=9%  Similarity=0.212  Sum_probs=69.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....++|||+|||+++|+++|+++|++||.| .|++    +++++|||||+|.+.++|++||+ +++..|.++.|.|..+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3567899999999999999999999999965 6653    57789999999999999999995 7999999999999988


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .+..
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.33  E-value=6.8e-13  Score=127.53  Aligned_cols=120  Identities=13%  Similarity=0.067  Sum_probs=69.1

Q ss_pred             cEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe
Q 003463          190 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  269 (818)
Q Consensus       190 G~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~  269 (818)
                      |+||.+|.-.+.+..++..+... ..+....-.....  ..........+|||+|||+++|++||+++|++|| |++|++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~--~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i   77 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDS--EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI   77 (139)
T ss_dssp             ----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCc--ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE
Confidence            56777777777766666543322 2222221111111  1111223456899999999999999999999999 668865


Q ss_pred             ----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          270 ----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       270 ----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                          .++++|||||+|.+.++|++|| .+|+..|.|+.|+|..+.+...
T Consensus        78 ~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           78 EIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence                3567899999999999999999 7999999999999999887653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.33  E-value=3.5e-12  Score=120.24  Aligned_cols=79  Identities=16%  Similarity=0.256  Sum_probs=69.5

Q ss_pred             CCCcE--EEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccE-EEEEEccHHHHHHHHHHhcCccccc--cccccccc
Q 003463          150 HPSRT--LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFS  224 (818)
Q Consensus       150 ~~srt--LfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~-AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~a  224 (818)
                      .++++  |||+||++.+++++|+++|++||.|.+|++..+ .|| |||+|.+.++|++|++.|+|..|.|  ++|+|.|+
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            34554  679999999999999999999999999986444 496 9999999999999999999999987  68999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus       100 k~~~l  104 (124)
T 2e5i_A          100 RPTRL  104 (124)
T ss_dssp             SCSCC
T ss_pred             cCCcc
Confidence            88764

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=9.2e-13  Score=115.60  Aligned_cols=79  Identities=24%  Similarity=0.452  Sum_probs=68.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      .++++|||+|||.++++++|+++|++||.|..|++...++|||||+|.+.++|++|+..  ...+.+++|+|.++.++..
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCC
Confidence            45799999999999999999999999999999998777899999999999999865432  3456899999999987654


Q ss_pred             C
Q 003463          230 P  230 (818)
Q Consensus       230 ~  230 (818)
                      .
T Consensus        81 ~   81 (88)
T 1wf0_A           81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=1.6e-12  Score=118.03  Aligned_cols=77  Identities=13%  Similarity=0.187  Sum_probs=68.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....+|||+|||+++|++||+++|++||.| +|++    +++++|||||+|.+.++|++||+ +|+..|.|+.|+|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            345699999999999999999999999955 7754    45678999999999999999995 89999999999999987


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      +..
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            655

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.32  E-value=9.9e-13  Score=122.44  Aligned_cols=76  Identities=18%  Similarity=0.172  Sum_probs=68.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCC---eEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~---I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ...+|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++||+ ||+..|.|+.|+|.+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFK   94 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEE
Confidence            4578999999999999999999999998   777764    35678999999999999999999 999999999999999


Q ss_pred             cCCC
Q 003463          309 SRPG  312 (818)
Q Consensus       309 a~~~  312 (818)
                      +.++
T Consensus        95 a~~~   98 (118)
T 2db1_A           95 SHRT   98 (118)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8643

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=1.3e-12  Score=114.67  Aligned_cols=78  Identities=19%  Similarity=0.328  Sum_probs=66.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCccc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~r  315 (818)
                      ..++|||+|||.++++++|+++|++||.|.+|++...++|||||+|.+.++|++|+.  ....+.|++|+|.+++++..+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCCCC
Confidence            357899999999999999999999999999999877789999999999999976433  133558999999999887643

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=6.6e-13  Score=122.64  Aligned_cols=78  Identities=14%  Similarity=0.169  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCE-EEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I-~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||+++|+++|+++|+.||.| ..|++    +++++|||||+|.+.++|++||+. ++..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            4567899999999999999999999999999 56653    467899999999999999999996 99999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      +.++
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.99  E-value=1.5e-13  Score=126.98  Aligned_cols=79  Identities=23%  Similarity=0.319  Sum_probs=71.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEE--------EEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~--------vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      ..++|||+|||.++++++|+++|++||.|..        |++     ++.++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4578999999999999999999999999988        644     356789999999999999999999999999999


Q ss_pred             eEEEEecCCCcc
Q 003463          303 RIKLEPSRPGGA  314 (818)
Q Consensus       303 ~L~V~~a~~~~~  314 (818)
                      +|+|++++++..
T Consensus        86 ~l~V~~a~~~~~   97 (116)
T 2lcw_A           86 PIKVSFATRRAD   97 (116)
Confidence            999999987654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=6e-13  Score=124.67  Aligned_cols=77  Identities=17%  Similarity=0.205  Sum_probs=68.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEE---E--ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI---R--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v---r--~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||+++|+++|+++|++||.|..+   .  .++.++|||||+|.+.++|.+||+ |||..|.|+.|+|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            45799999999999999999999999998652   1  356678999999999999999999 99999999999999987


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus       103 ~~~  105 (124)
T 1wel_A          103 KKG  105 (124)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            643

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.31  E-value=1.4e-12  Score=135.59  Aligned_cols=78  Identities=15%  Similarity=0.218  Sum_probs=71.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccC--CeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG--~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ...+|||+||++.+|+++|+++|++||  .|++|++     +++++|||||+|.+.++|++||+.|||+.|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            456899999999999999999999999  9999975     567789999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003463          309 SRPGG  313 (818)
Q Consensus       309 a~~~~  313 (818)
                      +++..
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            98654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=3.8e-12  Score=117.24  Aligned_cols=74  Identities=16%  Similarity=0.266  Sum_probs=67.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...+|||+|||+++|++||+++|++| .|..|++    .++++|||||+|.+.++|++|| .||+..|.||.|.|..+.+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            34689999999999999999999999 8888876    3567899999999999999999 6999999999999988754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.31  E-value=8.3e-13  Score=119.00  Aligned_cols=79  Identities=22%  Similarity=0.482  Sum_probs=70.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +.+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++  ++..+.|+.|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            445789999999999999999999999999999884    56789999999999999999999  899999999999988


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            76543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.98  E-value=1.8e-13  Score=126.59  Aligned_cols=82  Identities=22%  Similarity=0.370  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--------EEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~--------v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..        |++     +++++|||||+|.+.++|++|++.|++..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            356799999999999999999999999999987        552     4678999999999999999999999999999


Q ss_pred             cccccccccCCCCCC
Q 003463          216 RRKLDIHFSIPKDNP  230 (818)
Q Consensus       216 gr~L~V~~a~pk~~~  230 (818)
                      |++|+|.++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.31  E-value=1e-12  Score=119.93  Aligned_cols=78  Identities=15%  Similarity=0.102  Sum_probs=69.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCC---eEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~---I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      ....+|||+|||+++|+++|+++|+.||.   |..|++.    +.++|||||+|.+.++|++||+ +++..+.|+.|+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            35578999999999999999999999998   8888652    5678999999999999999999 99999999999999


Q ss_pred             ecCCCc
Q 003463          308 PSRPGG  313 (818)
Q Consensus       308 ~a~~~~  313 (818)
                      ++.++.
T Consensus        88 ~a~~~~   93 (107)
T 2lmi_A           88 EINNED   93 (107)
T ss_dssp             ECCHHH
T ss_pred             ECCHHH
Confidence            987643

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.31  E-value=2.5e-12  Score=119.06  Aligned_cols=71  Identities=14%  Similarity=0.188  Sum_probs=62.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...++|||+|||.++++++|+++|++||+|..|.+...  |||||+|.+.++|++||+.|++..|.|+.|+|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            35689999999999999999999999999999987544  999999999999999999999999999994433

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.30  E-value=6.2e-13  Score=124.57  Aligned_cols=77  Identities=9%  Similarity=0.198  Sum_probs=68.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE---EE--eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~---v~--~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||+++|+++|+++|+.||.|..   +.  .+++++|||||+|.+.++|++||+ +++..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            345689999999999999999999999998754   22  367889999999999999999999 999999999999998


Q ss_pred             cCC
Q 003463          224 SIP  226 (818)
Q Consensus       224 a~p  226 (818)
                      +.+
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            864

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.30  E-value=1e-12  Score=111.40  Aligned_cols=70  Identities=19%  Similarity=0.469  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +|||+|||.++++++|+++|++||+|..+.+     +++++|||||+|.+.++|++|++ +++..+.|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            5999999999999999999999999999874     36789999999999999999999 4899999999999864

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.30  E-value=2.3e-12  Score=133.83  Aligned_cols=76  Identities=16%  Similarity=0.237  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG--~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..++|||+|||+++|+++|+++|++||  .|..|++     +++++|||||+|.+.++|++||+.|++..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            467999999999999999999999999  9999884     678999999999999999999999999999999999999


Q ss_pred             cCC
Q 003463          224 SIP  226 (818)
Q Consensus       224 a~p  226 (818)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.30  E-value=5.9e-12  Score=109.69  Aligned_cols=71  Identities=21%  Similarity=0.383  Sum_probs=65.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhcc----C-------CeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAY----G-------EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~f----G-------~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                      ..++|||+|||.++++++|+++|++|    |       .|.++++. ..+|||||+|.+.++|.+|+ .|||..+.|++|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~-~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            45789999999999999999999999    8       89999885 45899999999999999999 999999999999


Q ss_pred             EEEe
Q 003463          305 KLEP  308 (818)
Q Consensus       305 ~V~~  308 (818)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9973

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.29  E-value=1.1e-12  Score=122.13  Aligned_cols=76  Identities=7%  Similarity=0.115  Sum_probs=68.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~---I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...++|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            45789999999999999999999999998   666652    47789999999999999999999 99999999999998


Q ss_pred             ccCC
Q 003463          223 FSIP  226 (818)
Q Consensus       223 ~a~p  226 (818)
                      ++.+
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.29  E-value=6.8e-12  Score=125.29  Aligned_cols=78  Identities=21%  Similarity=0.297  Sum_probs=71.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...+|||+|||+.+++++|+++|++||.|+.|++.    +.++|||||+|.+.++|++|++.|||..|.|+.|+|+++.+
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~  166 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  166 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            45699999999999999999999999999999763    55789999999999999999999999999999999999976


Q ss_pred             Cc
Q 003463          312 GG  313 (818)
Q Consensus       312 ~~  313 (818)
                      ..
T Consensus       167 ~~  168 (177)
T 2f3j_A          167 QI  168 (177)
T ss_dssp             GG
T ss_pred             CC
Confidence            54

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.29  E-value=4.3e-12  Score=110.52  Aligned_cols=72  Identities=18%  Similarity=0.387  Sum_probs=66.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  218 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~f----G-------~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~  218 (818)
                      .+.++|||+|||.++++++|+++|++|    |       .|..+++. +.+|||||+|.+.++|++|+ .|++..+.|+.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~-~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            457899999999999999999999999    8       99999864 45999999999999999999 89999999999


Q ss_pred             ccccc
Q 003463          219 LDIHF  223 (818)
Q Consensus       219 L~V~~  223 (818)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99863

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.29  E-value=6.9e-12  Score=126.92  Aligned_cols=114  Identities=13%  Similarity=0.160  Sum_probs=86.9

Q ss_pred             cHHHHHHHHHHh--cCcccccccccccccCCCCCCCC-----CCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec
Q 003463          198 DIRAARTAMRAL--QNKPLRRRKLDIHFSIPKDNPSD-----KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET  270 (818)
Q Consensus       198 d~e~A~~Al~~L--ng~~l~gr~L~V~~a~pk~~~~~-----~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~  270 (818)
                      +.+.+..|++..  ....+.+....|........+..     .....++|||+|||.++|+++|+++|++||.|..|++.
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            567778888766  44455555555554422222111     12345799999999999999999999999999999763


Q ss_pred             ----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          271 ----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       271 ----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                          +..+|||||+|.+.++|.+|+..+ +..+.|++|+|.+++.-
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence                567899999999999999999855 56999999999997653

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.28  E-value=1.8e-12  Score=118.37  Aligned_cols=78  Identities=9%  Similarity=0.041  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~---I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ....++|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++|++ +++..+.|+.|+|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            346789999999999999999999999998   777763    36789999999999999999999 9999999999999


Q ss_pred             cccCCC
Q 003463          222 HFSIPK  227 (818)
Q Consensus       222 ~~a~pk  227 (818)
                      .++.++
T Consensus        87 ~~a~~~   92 (107)
T 2lmi_A           87 YEINNE   92 (107)
T ss_dssp             EECCHH
T ss_pred             EECCHH
Confidence            987653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.28  E-value=7.4e-12  Score=130.66  Aligned_cols=80  Identities=19%  Similarity=0.309  Sum_probs=70.6

Q ss_pred             CCCccceeeecCCCCC---------CHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCcc-----
Q 003463          234 DLNQGTLVVFNLDPSV---------SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-----  299 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~v---------teedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i-----  299 (818)
                      ....++|||+||+..+         ++++|+++|++||.|.+|++. .++|||||+|.+.++|+.|+++|+|..|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            3456799999999998         799999999999999999985 4689999999999999999999999999     


Q ss_pred             -------CCceEEEEecCCCcc
Q 003463          300 -------AGKRIKLEPSRPGGA  314 (818)
Q Consensus       300 -------~Gr~L~V~~a~~~~~  314 (818)
                             .|+.|.|.||+....
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC----
T ss_pred             ccccccCCCCEEEEEEccCCCC
Confidence                   899999999987654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.28  E-value=1.7e-12  Score=124.34  Aligned_cols=76  Identities=7%  Similarity=0.093  Sum_probs=68.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~---I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ...++|||+|||+++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            45789999999999999999999999998   666552    47789999999999999999999 99999999999998


Q ss_pred             ccCC
Q 003463          223 FSIP  226 (818)
Q Consensus       223 ~a~p  226 (818)
                      ++.+
T Consensus       121 ~a~~  124 (136)
T 2hgl_A          121 KSHR  124 (136)
T ss_dssp             ECCH
T ss_pred             ECCh
Confidence            8754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.27  E-value=5.9e-12  Score=125.74  Aligned_cols=79  Identities=22%  Similarity=0.417  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+    +++++|||||+|.+.++|++|++.|++..|.|+.|+|.++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999985    3678999999999999999999999999999999999998


Q ss_pred             CCC
Q 003463          225 IPK  227 (818)
Q Consensus       225 ~pk  227 (818)
                      .+.
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.27  E-value=2.3e-12  Score=116.11  Aligned_cols=77  Identities=25%  Similarity=0.473  Sum_probs=69.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++  ++..+.|+.|.|.++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            34579999999999999999999999999999976    44568999999999999999998  9999999999999987


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            654

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.25  E-value=3.4e-12  Score=122.69  Aligned_cols=78  Identities=9%  Similarity=0.200  Sum_probs=68.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....++|||+|||+++|+++|+++|++|| |..|++    .++++|||||+|.+.++|++|| .+++..|.++.|.|..+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999 557773    4678999999999999999999 68999999999999988


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .++.
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7654

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.24  E-value=9e-12  Score=117.73  Aligned_cols=76  Identities=13%  Similarity=0.193  Sum_probs=67.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEE--EEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIR--TLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~--~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ....++|||+|||+++|+++|+++|++| .|.  .|++    .++++|||||+|.+.++|++|++. ++..|.|+.|+|.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~  116 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF  116 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEE
Confidence            3457899999999999999999999999 566  7763    467899999999999999999994 7899999999998


Q ss_pred             ccCC
Q 003463          223 FSIP  226 (818)
Q Consensus       223 ~a~p  226 (818)
                      .+.+
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.24  E-value=4.2e-12  Score=116.95  Aligned_cols=74  Identities=8%  Similarity=0.170  Sum_probs=66.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..++|||+|||+++|+++|+++|+.| .|..|++    .++++|||||+|.+.++|++|+ .+++..|.|+.|.|..+.+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            35799999999999999999999999 8888874    4678999999999999999999 5899999999999987643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=3.1e-12  Score=120.36  Aligned_cols=76  Identities=20%  Similarity=0.204  Sum_probs=66.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCe----EEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV----KEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I----~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      ...+|||+|||+++|++||+++|++||.|    ..|++    +++++|||||+|.+.++|++|++. |+..|.|+.|+|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            34689999999999999999999999975    45543    566789999999999999999986 9999999999999


Q ss_pred             ecCCC
Q 003463          308 PSRPG  312 (818)
Q Consensus       308 ~a~~~  312 (818)
                      .+.++
T Consensus       101 ~a~~~  105 (123)
T 2dha_A          101 RSTAA  105 (123)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=4.9e-12  Score=119.03  Aligned_cols=76  Identities=17%  Similarity=0.214  Sum_probs=66.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCE----EEEE----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDI----RTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I----~~v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ...++|||+|||+++|+++|+++|++||.|    ..|.    .+++++|||||+|.+.++|++|++. ++..|.++.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            356899999999999999999999999975    3443    2678899999999999999999996 999999999998


Q ss_pred             cccCC
Q 003463          222 HFSIP  226 (818)
Q Consensus       222 ~~a~p  226 (818)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.21  E-value=1.9e-11  Score=112.75  Aligned_cols=72  Identities=15%  Similarity=0.302  Sum_probs=60.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----C---CCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~---~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      ..+++|||+|||+++++++|+++|++||.|. +.+     +   ++++|||||+|.+.++|++|++.|++  +.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEEe
Confidence            4578999999999999999999999999999 552     2   57899999999999999999998842  56666655


Q ss_pred             ccc
Q 003463          222 HFS  224 (818)
Q Consensus       222 ~~a  224 (818)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.21  E-value=1.1e-11  Score=117.16  Aligned_cols=75  Identities=23%  Similarity=0.286  Sum_probs=66.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeE--EEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVK--EIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~--~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...+|||+|||+++|+++|+++|++| .|+  .|++    .++++|||||+|.+.++|++||+ +++..|.||.|+|..+
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            45789999999999999999999999 566  7765    35679999999999999999998 5789999999999988


Q ss_pred             CCC
Q 003463          310 RPG  312 (818)
Q Consensus       310 ~~~  312 (818)
                      .++
T Consensus       119 ~~~  121 (126)
T 2hgm_A          119 SQE  121 (126)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.21  E-value=3.3e-11  Score=111.14  Aligned_cols=78  Identities=14%  Similarity=0.206  Sum_probs=65.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----c---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----T---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      ..++|||+|||+++|+++|+++|++||.|. +++     +   +.++|||||+|.+.++|++|++.|+  .+.|+.|.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            457899999999999999999999999999 643     2   4779999999999999999999994  4788888887


Q ss_pred             ecCCCcccc
Q 003463          308 PSRPGGARR  316 (818)
Q Consensus       308 ~a~~~~~r~  316 (818)
                      .+.+...+.
T Consensus        84 ~~~~~~~~~   92 (114)
T 2dnl_A           84 SSPTIKDKP   92 (114)
T ss_dssp             CCSSSCSEE
T ss_pred             cCCCcCCCe
Confidence            766554443

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.20  E-value=1.9e-11  Score=127.66  Aligned_cols=81  Identities=21%  Similarity=0.374  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCCC---------cHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccc-----
Q 003463          149 EHPSRTLFVRNINSNV---------EDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-----  214 (818)
Q Consensus       149 e~~srtLfV~NLP~~v---------TEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l-----  214 (818)
                      ....++|||+||+.++         +|++|+++|++||+|.+|++. .++|||||+|.+.++|+.|+++|++..|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            4568999999999998         799999999999999999864 5799999999999999999999999999     


Q ss_pred             -------ccccccccccCCCCCC
Q 003463          215 -------RRRKLDIHFSIPKDNP  230 (818)
Q Consensus       215 -------~gr~L~V~~a~pk~~~  230 (818)
                             .|+.|.|.|+....++
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC-----
T ss_pred             ccccccCCCCEEEEEEccCCCCH
Confidence                   8999999999876544

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.20  E-value=5.5e-11  Score=109.41  Aligned_cols=79  Identities=16%  Similarity=0.283  Sum_probs=68.8

Q ss_pred             CCccceeeecCCCCCC-----------HHHHHHHhhccCCeEEEEe-cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          235 LNQGTLVVFNLDPSVS-----------NEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vt-----------eedL~~lFs~fG~I~~vr~-~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      ...++|+|.||....+           +++|+++|++||.|.+|.+ ...++|||||+|.+.++|.+|++.|||..+.|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   92 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   92 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            3567999999954332           5899999999999999976 345789999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 003463          303 RIKLEPSRPGG  313 (818)
Q Consensus       303 ~L~V~~a~~~~  313 (818)
                      +|+|.++.++.
T Consensus        93 ~l~v~~a~~~~  103 (112)
T 2dit_A           93 QITAQAWDGTT  103 (112)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCCC
Confidence            99999998764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.20  E-value=4.5e-11  Score=109.29  Aligned_cols=76  Identities=18%  Similarity=0.165  Sum_probs=66.6

Q ss_pred             CccceeeecCCC-----CCCHHHHHHHhhccCCeEEEEec------CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          236 NQGTLVVFNLDP-----SVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       236 ~~~tL~V~NLp~-----~vteedL~~lFs~fG~I~~vr~~------g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                      ..++|+|.||..     +-++++|+++|++||.|.+|++.      +.++|+|||+|.+.++|.+|++.|||+.+.||.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            356899999963     23789999999999999999762      3568999999999999999999999999999999


Q ss_pred             EEEecCC
Q 003463          305 KLEPSRP  311 (818)
Q Consensus       305 ~V~~a~~  311 (818)
                      +|.++.+
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999875

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=5.7e-11  Score=109.28  Aligned_cols=82  Identities=17%  Similarity=0.295  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCCCc-----------HHHHHHHhhcCCCEEEEEe-CCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          148 GEHPSRTLFVRNINSNVE-----------DSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vT-----------EeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                      ...++++|+|+||....+           +++|+++|++||.|..|.+ ...++|||||+|.+.++|++|++.|+|..+.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            456789999999944432           6899999999999999875 4457999999999999999999999999999


Q ss_pred             cccccccccCCCCC
Q 003463          216 RRKLDIHFSIPKDN  229 (818)
Q Consensus       216 gr~L~V~~a~pk~~  229 (818)
                      |++|.|.++.++..
T Consensus        91 gr~l~v~~a~~~~~  104 (112)
T 2dit_A           91 GRQITAQAWDGTTD  104 (112)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CcEEEEEEeCCCCC
Confidence            99999999987654

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.18  E-value=3.3e-11  Score=136.60  Aligned_cols=80  Identities=28%  Similarity=0.469  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.+||+++|+++|++||.|..|.+     +++++|||||+|.+.++|++||+.|+|..|.|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356789999999999999999999999999999875     567899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003463          224 SIPKD  228 (818)
Q Consensus       224 a~pk~  228 (818)
                      +.++.
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            98654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.15  E-value=7.9e-11  Score=107.65  Aligned_cols=77  Identities=16%  Similarity=0.240  Sum_probs=67.9

Q ss_pred             CCCcEEEEcCCCC-----CCcHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEEccHHHHHHHHHHhcCccccccc
Q 003463          150 HPSRTLFVRNINS-----NVEDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  218 (818)
Q Consensus       150 ~~srtLfV~NLP~-----~vTEeeLr~lFs~fG~I~~v~~~------~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~  218 (818)
                      .++++|+|+|+..     +-++++|+++|++||.|.+|.+.      ++++|||||+|.+.++|++|++.|+|..+.||.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            5789999999963     23789999999999999999841      467999999999999999999999999999999


Q ss_pred             ccccccCC
Q 003463          219 LDIHFSIP  226 (818)
Q Consensus       219 L~V~~a~p  226 (818)
                      |.|.++.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999854

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.14  E-value=3.8e-11  Score=112.91  Aligned_cols=77  Identities=16%  Similarity=0.292  Sum_probs=67.9

Q ss_pred             cceeeecC----CCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcC----HHH----HHHHHH--HcCCCc
Q 003463          238 GTLVVFNL----DPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYD----VRA----AEAALK--SLNRSD  298 (818)
Q Consensus       238 ~tL~V~NL----p~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d----~e~----A~~Ai~--~LnG~~  298 (818)
                      ..|||+||    |+.+++++|+++|+.||+|.++++     ++.++|||||+|.|    .++    |.+|+.  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            47999999    999999999999999999999964     77889999999996    333    899998  899999


Q ss_pred             cCCceEEEEecCCCcc
Q 003463          299 IAGKRIKLEPSRPGGA  314 (818)
Q Consensus       299 i~Gr~L~V~~a~~~~~  314 (818)
                      |.|++|+|.+-+.+..
T Consensus        83 I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           83 IMGFKFEVILNKHSIL   98 (136)
T ss_dssp             ETTEEEEEEECCTTHH
T ss_pred             ecCcEEEEEECcccHH
Confidence            9999999999887765

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=1.5e-10  Score=105.01  Aligned_cols=66  Identities=23%  Similarity=0.282  Sum_probs=60.1

Q ss_pred             CCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          247 PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       247 ~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ..+++++|+++|++||.|.+|++.+.++|||||+|.+.++|++|++.++  .+.|++|+|+|++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCCC
Confidence            5689999999999999999999988899999999999999999999755  46799999999987754

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.07  E-value=2.7e-10  Score=104.03  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=64.8

Q ss_pred             CccceeeecC--CCCCC--------HHHHHHHhhccCCeEEEEecC-------CCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          236 NQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRETP-------HKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       236 ~~~tL~V~NL--p~~vt--------eedL~~lFs~fG~I~~vr~~g-------~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ..+.|.|.|+  +..+.        ++||++.|++||.|.+|++..       .++|+|||+|.+.++|.+|++.|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3567889998  33332        379999999999999998732       468999999999999999999999999


Q ss_pred             cCCceEEEEecCC
Q 003463          299 IAGKRIKLEPSRP  311 (818)
Q Consensus       299 i~Gr~L~V~~a~~  311 (818)
                      +.||+|+|.|+..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999864

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.07  E-value=1.9e-10  Score=116.38  Aligned_cols=75  Identities=12%  Similarity=0.318  Sum_probs=67.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..++|||+|||.++++++|+++|++||.|..|++    .++++|||||+|.+.++|++|++.+ +..+.|+.|.|.+...
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            3589999999999999999999999999999974    4678999999999999999999865 5689999999998654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.05  E-value=8.2e-11  Score=110.69  Aligned_cols=73  Identities=19%  Similarity=0.312  Sum_probs=64.6

Q ss_pred             cEEEEcCC----CCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEcc----HHH----HHHHHH--HhcCcc
Q 003463          153 RTLFVRNI----NSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYD----IRA----ARTAMR--ALQNKP  213 (818)
Q Consensus       153 rtLfV~NL----P~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d----~e~----A~~Al~--~Lng~~  213 (818)
                      ++|||+||    |+.+++++|+++|+.||+|.+|.     .+++++|||||+|.+    .++    |.+|++  .++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    99999999999999999999988     378999999999996    333    889988  789999


Q ss_pred             cccccccccccC
Q 003463          214 LRRRKLDIHFSI  225 (818)
Q Consensus       214 l~gr~L~V~~a~  225 (818)
                      |.|++|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=1.2e-09  Score=98.98  Aligned_cols=75  Identities=19%  Similarity=0.282  Sum_probs=63.8

Q ss_pred             CcEEEEcCCC-------CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          152 SRTLFVRNIN-------SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       152 srtLfV~NLP-------~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .++|.|.-..       .++++++|+++|++||+|..|.+.++++|||||+|.+.++|++|++.+++  +.+++|+|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            4456665443       56899999999999999999998788999999999999999999997544  67999999998


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .++.
T Consensus        88 ~~~~   91 (100)
T 2d9o_A           88 EGQP   91 (100)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7654

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.02  E-value=4.3e-10  Score=102.70  Aligned_cols=77  Identities=17%  Similarity=0.375  Sum_probs=67.0

Q ss_pred             CCCcEEEEcCC--CCCCc--------HHHHHHHhhcCCCEEEEEeC-------CCcccEEEEEEccHHHHHHHHHHhcCc
Q 003463          150 HPSRTLFVRNI--NSNVE--------DSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMRALQNK  212 (818)
Q Consensus       150 ~~srtLfV~NL--P~~vT--------EeeLr~lFs~fG~I~~v~~~-------~ksrG~AFV~F~d~e~A~~Al~~Lng~  212 (818)
                      .|++.|.|+|+  |.++.        +++|++.|++||.|.+|++.       .+++|+|||+|.+.++|++|++.|+|+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            57999999998  44443        36899999999999999852       246899999999999999999999999


Q ss_pred             ccccccccccccCC
Q 003463          213 PLRRRKLDIHFSIP  226 (818)
Q Consensus       213 ~l~gr~L~V~~a~p  226 (818)
                      .+.||.|.|.|+.+
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999998753

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.98  E-value=1.7e-10  Score=105.14  Aligned_cols=68  Identities=28%  Similarity=0.401  Sum_probs=58.3

Q ss_pred             eecCCCCCCHHHHHHHh------------hccCCeEEEEec----CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          242 VFNLDPSVSNEDLRQIF------------GAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       242 V~NLp~~vteedL~~lF------------s~fG~I~~vr~~----g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      +.||+..+++++|++.|            ++||.|.+|++.    ++++|||||+|.+.++|.+|++.|||+.+.||+|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            45677777777766666            999999999874    34589999999999999999999999999999999


Q ss_pred             EEec
Q 003463          306 LEPS  309 (818)
Q Consensus       306 V~~a  309 (818)
                      |+|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.98  E-value=6.7e-10  Score=121.74  Aligned_cols=76  Identities=18%  Similarity=0.338  Sum_probs=65.6

Q ss_pred             CCCCCcEEEEcC--CCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccc---cc--ccc
Q 003463          148 GEHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR---RR--KLD  220 (818)
Q Consensus       148 ~e~~srtLfV~N--LP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~---gr--~L~  220 (818)
                      ...|+++|||+|  |+..+||++|+++|++||+|.+|.+. .+||||||+|.+.++|++|++.|||..+.   |+  .|+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~-~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC-TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            356899999999  58899999999999999999999764 47899999999999999999999999873   33  466


Q ss_pred             cccc
Q 003463          221 IHFS  224 (818)
Q Consensus       221 V~~a  224 (818)
                      |.|+
T Consensus        93 ~~~~   96 (345)
T 3tht_A           93 LNFV   96 (345)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            6664

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.97  E-value=8.1e-10  Score=121.08  Aligned_cols=74  Identities=23%  Similarity=0.358  Sum_probs=65.6

Q ss_pred             Cccceeeec--CCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC---Cc--eEEEEe
Q 003463          236 NQGTLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA---GK--RIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~N--Lp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~---Gr--~L~V~~  308 (818)
                      ...+|||+|  |+..+|+++|+++|++||+|++|++.. +||||||+|.+.++|++|+++|||+++.   |+  .|.|.|
T Consensus        17 ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~   95 (345)
T 3tht_A           17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF   95 (345)
T ss_dssp             CCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEE
Confidence            456899999  578999999999999999999998854 7899999999999999999999999873   44  688888


Q ss_pred             cC
Q 003463          309 SR  310 (818)
Q Consensus       309 a~  310 (818)
                      +.
T Consensus        96 ~~   97 (345)
T 3tht_A           96 VE   97 (345)
T ss_dssp             CS
T ss_pred             ee
Confidence            75

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.94  E-value=2.1e-09  Score=99.77  Aligned_cols=76  Identities=18%  Similarity=0.143  Sum_probs=64.1

Q ss_pred             CccceeeecCCCCC----------CHHHHHHHhhccCCeEEEEecCC-CCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          236 NQGTLVVFNLDPSV----------SNEDLRQIFGAYGEVKEIRETPH-KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       236 ~~~tL~V~NLp~~v----------teedL~~lFs~fG~I~~vr~~g~-srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                      ..++|.|.|+=..-          .++||++.|++||.|.+|.+... .+|++||+|.+.++|.+|++.|||+.+.||.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            35578888874322          23689999999999999987543 48999999999999999999999999999999


Q ss_pred             EEEecCC
Q 003463          305 KLEPSRP  311 (818)
Q Consensus       305 ~V~~a~~  311 (818)
                      +|.|+..
T Consensus        86 ~v~~~~~   92 (114)
T 3s6e_A           86 TAAYVPL   92 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEEEcH
Confidence            9999854

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.91  E-value=1.6e-09  Score=101.06  Aligned_cols=75  Identities=19%  Similarity=0.277  Sum_probs=63.5

Q ss_pred             ccceeeecCCC--CC---CHHHHHHHhhccCCeEEEEec---------CCCCceEEEEEcCHHHHHHHHHHcCCCccCCc
Q 003463          237 QGTLVVFNLDP--SV---SNEDLRQIFGAYGEVKEIRET---------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  302 (818)
Q Consensus       237 ~~tL~V~NLp~--~v---teedL~~lFs~fG~I~~vr~~---------g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr  302 (818)
                      .++|+|.|+-.  ++   .++||++.|++||.|.+|++.         +.++|++||+|.+.++|.+|++.|||+.+.||
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR   99 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR   99 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            46889999842  22   368999999999999998652         23468999999999999999999999999999


Q ss_pred             eEEEEecCC
Q 003463          303 RIKLEPSRP  311 (818)
Q Consensus       303 ~L~V~~a~~  311 (818)
                      .|+|.|+..
T Consensus       100 ~i~v~~~~~  108 (118)
T 3ue2_A          100 KVVAEVYDQ  108 (118)
T ss_dssp             ECEEEEECH
T ss_pred             EEEEEEcCh
Confidence            999999854

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.90  E-value=4.9e-10  Score=102.09  Aligned_cols=68  Identities=21%  Similarity=0.366  Sum_probs=59.4

Q ss_pred             EcCCCCCCcHHHHHHHh------------hcCCCEEEEEeC----CCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          157 VRNINSNVEDSELRALF------------EQYGDIRTLYTA----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       157 V~NLP~~vTEeeLr~lF------------s~fG~I~~v~~~----~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      +.+||..+++++|++.|            ++||+|.+|++.    ++++|||||+|.+.++|++|++.|+|..+.|++|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56677778888777666            999999999853    45799999999999999999999999999999999


Q ss_pred             cccc
Q 003463          221 IHFS  224 (818)
Q Consensus       221 V~~a  224 (818)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9886

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.86  E-value=3.6e-09  Score=98.71  Aligned_cols=75  Identities=13%  Similarity=0.185  Sum_probs=65.2

Q ss_pred             CCcEEEEcCCCC--C---CcHHHHHHHhhcCCCEEEEEeC---------CCcccEEEEEEccHHHHHHHHHHhcCccccc
Q 003463          151 PSRTLFVRNINS--N---VEDSELRALFEQYGDIRTLYTA---------CKHRGFVMISYYDIRAARTAMRALQNKPLRR  216 (818)
Q Consensus       151 ~srtLfV~NLP~--~---vTEeeLr~lFs~fG~I~~v~~~---------~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g  216 (818)
                      ++++|+|+|+-.  +   -.+++|++.|++||.|.+|++.         ++++|++||+|.+.++|++|++.|+|..+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            789999999842  2   2368999999999999998731         2467999999999999999999999999999


Q ss_pred             ccccccccC
Q 003463          217 RKLDIHFSI  225 (818)
Q Consensus       217 r~L~V~~a~  225 (818)
                      |.|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.79  E-value=9.1e-09  Score=95.42  Aligned_cols=76  Identities=14%  Similarity=0.208  Sum_probs=64.9

Q ss_pred             CCCcEEEEcCCCCCCc----------HHHHHHHhhcCCCEEEEEeCCC-cccEEEEEEccHHHHHHHHHHhcCccccccc
Q 003463          150 HPSRTLFVRNINSNVE----------DSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNKPLRRRK  218 (818)
Q Consensus       150 ~~srtLfV~NLP~~vT----------EeeLr~lFs~fG~I~~v~~~~k-srG~AFV~F~d~e~A~~Al~~Lng~~l~gr~  218 (818)
                      .+++.|.++|+=..-.          +++|++.|++||.|.+|.+... .+|+|||+|.+.++|++|++.|+|..+.||.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~   84 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4788999999833211          3578999999999999986433 5899999999999999999999999999999


Q ss_pred             ccccccC
Q 003463          219 LDIHFSI  225 (818)
Q Consensus       219 L~V~~a~  225 (818)
                      |.|.|+.
T Consensus        85 i~v~~~~   91 (114)
T 3s6e_A           85 ITAAYVP   91 (114)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEEc
Confidence            9999874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.70  E-value=3.7e-08  Score=87.04  Aligned_cols=75  Identities=25%  Similarity=0.406  Sum_probs=63.4

Q ss_pred             CCccceeeecCC----CCCCH----HHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEE
Q 003463          235 LNQGTLVVFNLD----PSVSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  306 (818)
Q Consensus       235 ~~~~tL~V~NLp----~~vte----edL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V  306 (818)
                      +...||+|.-.+    .++-.    .+|.+.|++||+|..+|+..   +.+||+|.+.++|.+||+ |||..+.||.|+|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV   80 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITI   80 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEE
Confidence            345688888776    23333    67999999999999999864   349999999999999998 9999999999999


Q ss_pred             EecCCCc
Q 003463          307 EPSRPGG  313 (818)
Q Consensus       307 ~~a~~~~  313 (818)
                      +++++.-
T Consensus        81 ~lkt~dW   87 (91)
T 2dnr_A           81 ALKSPSG   87 (91)
T ss_dssp             EECCCSS
T ss_pred             EeCCCCc
Confidence            9998764

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=98.64  E-value=6.3e-08  Score=85.95  Aligned_cols=84  Identities=21%  Similarity=0.294  Sum_probs=71.5

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcccEEE-eeeccccc-ceeEEEEEecCCcccHHHHHHHhcCCcccCCC-CccE
Q 003463          655 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLY-LPIDFKNK-CNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN-SEKV  731 (818)
Q Consensus       655 TtvMirNIPn~~~~~~l~~~id~~~~~~ydf~Y-lp~d~~~~-~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~-s~k~  731 (818)
                      |.|.||++|..+|++.+++.|+...  ++||+| .|-+...+ +--+.|||||++++++..|.+.|+|+.|..-+ .+-.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~--~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~   79 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMP--EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCC--CEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcc--cceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEee
Confidence            7899999999999999999999764  688885 57776544 44578999999999999999999999998653 4577


Q ss_pred             EEEEeeecc
Q 003463          732 ASLAYARIQ  740 (818)
Q Consensus       732 ~~~~~A~iQ  740 (818)
                      +.|.||--|
T Consensus        80 a~VE~AP~q   88 (91)
T 1uw4_A           80 AIVEFAPFQ   88 (91)
T ss_dssp             CEEEECSSC
T ss_pred             eEEEEcCCC
Confidence            889999877

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=1.9e-07  Score=87.29  Aligned_cols=85  Identities=19%  Similarity=0.159  Sum_probs=70.6

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcC-HHHHHHHHHHcC--CCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYD-VRAAEAALKSLN--RSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d-~e~A~~Ai~~Ln--G~~i~Gr~L~V~~a~~  311 (818)
                      ....|+|+||+.. ++.++|+++|++||+|..|++.... ..|||+|.+ .++|.+|+++|+  +..|.|..++++...-
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~G   95 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            4568999999999 9999999999999999999985433 479999999 899999999995  7799999999988764


Q ss_pred             Ccccchhhhcc
Q 003463          312 GGARRNLMLQL  322 (818)
Q Consensus       312 ~~~r~~~~~ql  322 (818)
                      ..++ .|+...
T Consensus        96 eeE~-~yw~Ki  105 (121)
T 1owx_A           96 EVEK-EALKKI  105 (121)
T ss_dssp             HHHH-HHHHHH
T ss_pred             HHHH-HHHHHH
Confidence            4433 344443

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=98.46  E-value=6e-08  Score=86.62  Aligned_cols=84  Identities=21%  Similarity=0.343  Sum_probs=69.7

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcccEE-Eeeecccccce-eEEEEEecCCcccHHHHHHHhcCCcccCCC-CccE
Q 003463          655 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL-YLPIDFKNKCN-VGYAFINMLSPLHIIPFYEAFNGKKWEKFN-SEKV  731 (818)
Q Consensus       655 TtvMirNIPn~~~~~~l~~~id~~~~~~ydf~-Ylp~d~~~~~n-~gyafin~~~~~~~~~f~~~f~g~~w~~~~-s~k~  731 (818)
                      -.|.||++|+.+|++.+++.|+....  .||+ |.|-|...+-+ -..|||||++++++..|.+.|+|+.|..-+ .+-.
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~--~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSS--EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCc--cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            47999999999999999999997654  4666 57777665433 367999999999999999999999998653 4578


Q ss_pred             EEEEeeecc
Q 003463          732 ASLAYARIQ  740 (818)
Q Consensus       732 ~~~~~A~iQ  740 (818)
                      +.|.||-.|
T Consensus        88 a~VE~APyq   96 (97)
T 2l08_A           88 AVVEFAPFQ   96 (97)
T ss_dssp             EEEEECCCC
T ss_pred             eEEEecCCC
Confidence            889999877

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.44  E-value=2.6e-07  Score=82.09  Aligned_cols=73  Identities=22%  Similarity=0.364  Sum_probs=61.7

Q ss_pred             CCccceeeecCCCC-----CCH----HHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          235 LNQGTLVVFNLDPS-----VSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       235 ~~~~tL~V~NLp~~-----vte----edL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      +...||+|.-++..     +-.    .+|.+.|.+||+|..+|+....   +||+|.+.++|.+||+ |||.++.||.|+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            45679999988743     222    5689999999999999986433   9999999999999998 999999999999


Q ss_pred             EEecCC
Q 003463          306 LEPSRP  311 (818)
Q Consensus       306 V~~a~~  311 (818)
                      |++..+
T Consensus        89 V~~k~~   94 (95)
T 1ufw_A           89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EeccCC
Confidence            998654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.38  E-value=9.2e-07  Score=82.63  Aligned_cols=73  Identities=15%  Similarity=0.137  Sum_probs=61.9

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEcc-HHHHHHHHHHhc--Ccccccccccccc
Q 003463          150 HPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD-IRAARTAMRALQ--NKPLRRRKLDIHF  223 (818)
Q Consensus       150 ~~srtLfV~NLP~~-vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d-~e~A~~Al~~Ln--g~~l~gr~L~V~~  223 (818)
                      .+.+.|||+||+.+ +++++|+++|++||+|..|.+.. ..-.|||.|.+ .++|+.|++.++  +..|.+..+.+..
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~-g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            45789999999999 99999999999999999998532 33479999999 899999999984  6778887766654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.30  E-value=9.5e-07  Score=78.06  Aligned_cols=73  Identities=21%  Similarity=0.322  Sum_probs=61.1

Q ss_pred             CCcEEEEcCCC----CCCcH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          151 PSRTLFVRNIN----SNVED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       151 ~srtLfV~NLP----~~vTE----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      |.-||+|.-.+    .++-+    .+|.+.|.+||+|..+++..   +.+||+|.+.++|.+|++ |+|..+.||.|+|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            56788888776    23434    67899999999999998643   239999999999999999 99999999999999


Q ss_pred             ccCCC
Q 003463          223 FSIPK  227 (818)
Q Consensus       223 ~a~pk  227 (818)
                      ++.|.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            98764

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.28  E-value=9.2e-07  Score=90.49  Aligned_cols=63  Identities=19%  Similarity=0.259  Sum_probs=56.4

Q ss_pred             CCHHHHHHHhhccCCeEEEEec---------CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          249 VSNEDLRQIFGAYGEVKEIRET---------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       249 vteedL~~lFs~fG~I~~vr~~---------g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      -.+++|++.|++||.|.++.+.         +.++|++||+|.+.++|.+|++.|||+.+.||.|+|.|+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            3568999999999999999762         26789999999999999999999999999999999999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.18  E-value=3.7e-06  Score=76.27  Aligned_cols=72  Identities=24%  Similarity=0.252  Sum_probs=65.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhcc-----CCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAY-----GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~f-----G~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ..++|-+.|||..+++..|+.+.++|     |.|+.|.+.+...| |+|+|.|...|.+|..+|+|.+|.|++|++.-
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~G-Aivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG-AIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTE-EEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCc-eEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            35689999999999999999999999     99999988666544 99999999999999999999999999999864

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.03  E-value=6.1e-06  Score=84.34  Aligned_cols=74  Identities=14%  Similarity=0.199  Sum_probs=61.6

Q ss_pred             CcEEEEcCCC-----CCCcHHHHHHHhhcCCCEEEEEe---------CCCcccEEEEEEccHHHHHHHHHHhcCcccccc
Q 003463          152 SRTLFVRNIN-----SNVEDSELRALFEQYGDIRTLYT---------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  217 (818)
Q Consensus       152 srtLfV~NLP-----~~vTEeeLr~lFs~fG~I~~v~~---------~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr  217 (818)
                      ++.+.+.++-     .+-.+++|++.|++||+|.++.+         +++++|++||+|.+.++|++|++.|+|+.+.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            4455555542     23456889999999999999984         227889999999999999999999999999999


Q ss_pred             cccccccC
Q 003463          218 KLDIHFSI  225 (818)
Q Consensus       218 ~L~V~~a~  225 (818)
                      .|.+.|+.
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999874

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.96  E-value=6.3e-06  Score=73.23  Aligned_cols=71  Identities=15%  Similarity=0.211  Sum_probs=58.8

Q ss_pred             CCcEEEEcCCCCC-----CcH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          151 PSRTLFVRNINSN-----VED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       151 ~srtLfV~NLP~~-----vTE----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      |.-||+|.-++.+     +-+    .+|.+.|.+||+|..+++....   +||+|.+.++|.+||+ |+|..+.||.|+|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V   89 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEEEE
Confidence            6789999988743     222    5688999999999998853322   9999999999999999 9999999999999


Q ss_pred             cccC
Q 003463          222 HFSI  225 (818)
Q Consensus       222 ~~a~  225 (818)
                      ++-.
T Consensus        90 ~~k~   93 (95)
T 1ufw_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            8754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.57  E-value=0.00011  Score=66.64  Aligned_cols=71  Identities=13%  Similarity=0.170  Sum_probs=63.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcC-----CCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~f-----G~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ..++|-+-+||-.++++.|+.+.+++     |.|+.|..-.. .+=|+|+|.|...|-+|.-+|+|..|.|++|++.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-CCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            46899999999999999999999999     99999876444 4459999999999999998999999999999875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.54  E-value=0.00059  Score=61.40  Aligned_cols=88  Identities=18%  Similarity=0.244  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhc-----CCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQ-----YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~-----fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|.|.|||.+++++.|.-+|+.     =|+|..+....   +-|+|+|.+.+.|++.++. ....|.+..|.|....
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAP   82 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCC
Confidence            4689999999999999999999996     26899987544   7799999999999999983 4788899999997665


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCC
Q 003463          226 PKDNPSDKDLNQGTLVVFNLDPSVS  250 (818)
Q Consensus       226 pk~~~~~~~~~~~tL~V~NLp~~vt  250 (818)
                      ++.        ..+|.+.+|++.++
T Consensus        83 ~~~--------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           83 PRA--------PARLLLQGLPPGTS   99 (104)
T ss_dssp             CCC--------CCCCCCCSCCCCCC
T ss_pred             CCC--------cceEeeecCCCCCC
Confidence            433        34799999998875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.52  E-value=0.0006  Score=61.37  Aligned_cols=83  Identities=24%  Similarity=0.310  Sum_probs=71.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhc-----cCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGA-----YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~-----fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..+|.|.|||+.+.++.|.-+|+.     =|.|..++..+   +-|+|+|.+.+.|++.++ -..+.|.|.+|.|....+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLA-QADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcCCC
Confidence            468999999999999999999987     26899998876   679999999999999997 237899999999999888


Q ss_pred             Ccccchhhhccc
Q 003463          312 GGARRNLMLQLN  323 (818)
Q Consensus       312 ~~~r~~~~~ql~  323 (818)
                      ....+.+++.+.
T Consensus        84 ~~~~r~ll~gl~   95 (104)
T 2dhx_A           84 RAPARLLLQGLP   95 (104)
T ss_dssp             CCCCCCCCCSCC
T ss_pred             CCcceEeeecCC
Confidence            888888877764

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.97  E-value=0.00087  Score=60.51  Aligned_cols=75  Identities=19%  Similarity=0.237  Sum_probs=62.4

Q ss_pred             cceeeecCCCCC-CH----HHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          238 GTLVVFNLDPSV-SN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       238 ~tL~V~NLp~~v-te----edL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ++|+|.||+.++ +.    +.++++|..|+++.....-+.-+ -..|.|.+.++|.+|...|++..+.|++|+|-|+.+.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            589999999866 32    56789999999888876543333 3789999999999999999999999999999999865


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        85 ~   85 (104)
T 1wey_A           85 H   85 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.49  E-value=0.0068  Score=56.09  Aligned_cols=75  Identities=16%  Similarity=0.201  Sum_probs=61.9

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCC-ceEEEEecCC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-KRIKLEPSRP  311 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G-r~L~V~~a~~  311 (818)
                      .....-|.|.+.|+.. ...|.+.|++||+|.+... .....+-.|+|.++.+|++||. .||..+.| -.|-|.+...
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d   96 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   96 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCC
Confidence            3445689999999885 6778899999999999987 3456799999999999999998 69999985 6677777643

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.40  E-value=0.0054  Score=55.34  Aligned_cols=76  Identities=20%  Similarity=0.226  Sum_probs=62.8

Q ss_pred             CcEEEEcCCCCCC-c----HHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNV-E----DSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~v-T----EeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .++|+|.||+.+| .    .+.++.+|..|+++.....- ++-.=..|.|.+.++|.+|...|++..+.|+.++|.|+.+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~l-kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeec-CcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            4689999998865 2    25778999999988776532 3444579999999999999999999999999999999875


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      ..
T Consensus        84 ~~   85 (104)
T 1wey_A           84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.59  E-value=0.029  Score=49.56  Aligned_cols=64  Identities=5%  Similarity=0.050  Sum_probs=52.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eCCC------cccEEEEEEccHHHHHHHHHHhcCccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK------HRGFVMISYYDIRAARTAMRALQNKPLRR  216 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-~~~k------srG~AFV~F~d~e~A~~Al~~Lng~~l~g  216 (818)
                      ++|.|++||+.+||+++.+.+..+.++.... ..|+      .-.-|+|.|.+.+++....+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            5799999999999999999999988765544 2222      23469999999999999999999988754

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.45  E-value=0.028  Score=50.06  Aligned_cols=55  Identities=18%  Similarity=0.303  Sum_probs=43.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      ...++| ++|+++...||.++|++||.|.--.++   ...|||-|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            345666 999999999999999999854333332   2469999999999999999763

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=94.33  E-value=0.031  Score=49.89  Aligned_cols=54  Identities=19%  Similarity=0.300  Sum_probs=43.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      ..++| ++|+++...||.++|++||.|.--.++   ...|||-|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEE---TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            35666 999999999999999999954333333   3469999999999999999765

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=94.20  E-value=0.054  Score=48.23  Aligned_cols=55  Identities=18%  Similarity=0.315  Sum_probs=45.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  210 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Ln  210 (818)
                      .+.++| ++|+++...||.++|+.||.|.--.+   ....|||.|.+.+.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            456677 99999999999999999996543223   34579999999999999999764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=94.11  E-value=0.057  Score=48.22  Aligned_cols=54  Identities=19%  Similarity=0.325  Sum_probs=44.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  210 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Ln  210 (818)
                      +.++| ++|+++...||.++|+.||.|.--.+   ....|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEE---ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            45566 99999999999999999995443223   35579999999999999999765

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.08  E-value=0.1  Score=46.53  Aligned_cols=72  Identities=11%  Similarity=0.088  Sum_probs=53.2

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-cCC------CCceEEEEEcCHHHHHHHHHHcCCCccCC-----ceEE
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPH------KRHHKFIEFYDVRAAEAALKSLNRSDIAG-----KRIK  305 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-~g~------srG~aFVeF~d~e~A~~Ai~~LnG~~i~G-----r~L~  305 (818)
                      -+|.|+.||+.+|++++.+.+++.-++..... .|+      .-.-|+|.|.+.++...-.+.++|..+-+     -+..
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            37999999999999999988887655433221 111      12348999999999999999999987654     2455


Q ss_pred             EEec
Q 003463          306 LEPS  309 (818)
Q Consensus       306 V~~a  309 (818)
                      |++|
T Consensus        90 VE~A   93 (97)
T 2l08_A           90 VEFA   93 (97)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            6665

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=94.07  E-value=0.13  Score=47.63  Aligned_cols=71  Identities=17%  Similarity=0.184  Sum_probs=56.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccc-cccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g-r~L~V~~a  224 (818)
                      ..+-|.|-+.|+.. ...|...|++||+|.+... ........|.|.+..+|++||. .||..|.+ --|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            35789999999885 6678889999999999875 3356799999999999999999 59988874 44555443

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.19  E-value=0.072  Score=49.96  Aligned_cols=71  Identities=18%  Similarity=0.264  Sum_probs=56.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEE-EEec----------------C--CCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRET----------------P--HKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~-vr~~----------------g--~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      .-|.|.+.|++. ...+.+.|++||.|.+ +...                +  ...++..|+|++..+|.+||. -||..
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            468889997765 4667889999999977 2211                1  135678999999999999998 69999


Q ss_pred             cCCceEEEEecC
Q 003463          299 IAGKRIKLEPSR  310 (818)
Q Consensus       299 i~Gr~L~V~~a~  310 (818)
                      |.|.-|-|.+..
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988888875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.58  E-value=0.052  Score=61.45  Aligned_cols=57  Identities=11%  Similarity=0.151  Sum_probs=44.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHH
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  293 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~  293 (818)
                      ..++|+|. .+..+++.+|.+.|++||.|.++........||.|||.+.+++..++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            34689998 7999999999999999999999988776677999999999998877653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.69  E-value=0.064  Score=60.71  Aligned_cols=56  Identities=9%  Similarity=0.273  Sum_probs=43.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHH
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR  207 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~  207 (818)
                      ..|+|+|. .|..+++.+|.++|++||+|.++.......-||.|+|.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            35899997 799999999999999999999998655555699999999999997765

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=85.82  E-value=0.48  Score=44.42  Aligned_cols=71  Identities=14%  Similarity=0.183  Sum_probs=52.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eC-------------C-----CcccEEEEEEccHHHHHHHHHHhcCc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TA-------------C-----KHRGFVMISYYDIRAARTAMRALQNK  212 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-~~-------------~-----ksrG~AFV~F~d~e~A~~Al~~Lng~  212 (818)
                      ..-|.|-+.|++.+ ..+.+.|++||.|.+-. ..             .     .......|+|.+..+|++||. .+|.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45677888876644 56778999999987732 11             0     135678999999999999999 5999


Q ss_pred             cccccccccccc
Q 003463          213 PLRRRKLDIHFS  224 (818)
Q Consensus       213 ~l~gr~L~V~~a  224 (818)
                      .|.|.-|-|...
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            998876666554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	818
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-19
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-14
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	9e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-10
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	9e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	9e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.001
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.002
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	7e-04
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	0.001
d1uw4a_	91	d.58.7.4 (A:) RNA processing protein UPF3x, RRM do	0.003

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.1 bits (209), Expect = 1e-19
 Identities = 34/171 (19%), Positives = 59/171 (34%), Gaps = 12/171 (7%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAM 206
            R LF+  ++    D  LR+ FEQ+G +            + RGF  ++Y  +     AM
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 207 RALQNKPLRRRKLDIHFSI-PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 265
            A  +K   R                   L    + V  +        LR  F  YG+++
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125

Query: 266 EI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
            I     R +  KR   F+ F D  + +  +       + G   ++  +  
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS 175

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 1e-16
 Identities = 23/111 (20%), Positives = 55/111 (49%), Gaps = 8/111 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKSLNR 296
            L + NL   ++ E++  IFG YG +++I    TP  R   ++ + D+  A+ A   L+ 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 297 SDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPP 347
            ++  + + +       A +    +++ + ++++ ++L+ + G  I   PP
Sbjct: 69  FNVCNRYLVVLYYNANRAFQ----KMDTKKKEEQLKLLKEKYG--INTDPP 113

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.2 bits (174), Expect = 1e-15
 Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--HRGFVMISYYDIRAARTAMRA 208
            +R L++RN+   +   E+  +F +YG IR +        RG   + Y DI  A+ A   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 209 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 237
           L    +  R L + +          D  +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKK 94

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.6 bits (170), Expect = 2e-15
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
           +L V +L P V+   L + F   G +  IR      T     + ++ F     AE AL +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 294 LNRSDIAGKRIKLEPSR 310
           +N   I GK +++  S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.9 bits (145), Expect = 5e-12
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRA 208
           +L+V +++ +V ++ L   F   G I            +  G+  +++     A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 209 LQNKPLRRRKLDIHFS 224
           +    ++ + + I +S
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.6 bits (170), Expect = 3e-15
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
           TL V NL    + E + ++F   G++K+I     K         F+E+Y    AE A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 294 LNRSDIAGKRIKLEPSRPGGARR 316
           +N + +  + I+ +        R
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGR 91

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.4 bits (154), Expect = 4e-13
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTA 205
            S TL+V N++    + ++  LF + GDI+ +            GF  + YY    A  A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 206 MRALQNKPLRRRKLDIHFSIPK 227
           MR +    L  R +   +    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 68.5 bits (167), Expect = 5e-15
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
            L+V  L   +++ +L  +F A G +   R     +T +   + F++F     ++ A+K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 294 LNRSDIAGKRIKLEPSRPG 312
           LN   +  KR+K+  +RPG
Sbjct: 64  LNGITVRNKRLKVSYARPG 82

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.3 bits (138), Expect = 5e-11
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTAM 206
           +  L V  +  ++ D EL ALF   G I T      ++      +  + +     ++ A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 207 RALQNKPLRRRKLDIHFSIP 226
           + L    +R ++L + ++ P
Sbjct: 62  KVLNGITVRNKRLKVSYARP 81

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.0 bits (166), Expect = 8e-15
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKS 293
           G L+V NLD  VS+ D++++F  +G +K+       +        + F     A  A+K 
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 294 LNRSDIAGKRIKLE 307
            N   + G+ + ++
Sbjct: 61  YNGVPLDGRPMNIQ 74

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.8 bits (129), Expect = 7e-10
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRT----LYTACKHRGFVMISYYDIRAARTAMRALQ 210
           L V N++  V D++++ LF ++G ++        + +  G   + +     A  AM+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 211 NKPLRRRKLDIHFS 224
             PL  R ++I   
Sbjct: 63  GVPLDGRPMNIQLV 76

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 68.1 bits (166), Expect = 1e-14
 Identities = 20/87 (22%), Positives = 41/87 (47%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA 289
            S K     TL+  NL  +++ ++L+++F    E++ + +    +   +IEF     AE 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 290 ALKSLNRSDIAGKRIKLEPSRPGGARR 316
            L+    ++I G+ + L  +   G  R
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 64.3 bits (156), Expect = 3e-13
 Identities = 18/81 (22%), Positives = 37/81 (45%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
            +RTL  +N++ N+ + EL+ +FE   +IR +    K +G   I +     A   +   Q
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
              +  R + ++++  K    
Sbjct: 75  GAEIDGRSVSLYYTGEKGGTR 95

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (163), Expect = 2e-14
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDV 284
           P  +     T+ V  LD  VS   L ++F   G V          T   + + F+EF   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 285 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
             A+ A+K ++   + GK I++  +      +NL
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAH--NKNL 93

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 3e-11
 Identities = 13/84 (15%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 205
              T++V  ++  V +  L  LF Q G      +       +H+G+  + +     A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           ++ +    L  + + ++ +   + 
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (163), Expect = 3e-14
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG---EVKEIRETPHKRHHKFIEFYDVRA 286
           PS +    G + + NLD S+ N+ L   F A+G     K + +    + + F+ F    A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 287 AEAALKSLNRSDIAGKRIKLEPSRP 311
           AE A++ +N   +  +++ +   + 
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRFKS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 12/79 (15%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRA 208
              +F++N++ ++++  L   F  +G     + +      +G+  + +    AA  A+  
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 209 LQNKPLRRRKLDIHFSIPK 227
           +    L  RK+ +     +
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (163), Expect = 4e-14
 Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 9/97 (9%)

Query: 226 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIE 280
           P DN S ++ +  T+    L   +   DL   F A G+V+++R      +   +   ++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 281 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
           F ++++   A+  L    + G  I ++ S+     +N
Sbjct: 67  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQA---EKN 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 9e-10
 Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAAR 203
           E  +RT+F   + + +   +L   F   G +R +         + +G   + + +I++  
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 204 TAMRALQNKPLRRRKLDIHFSIPKDN 229
                L  + L    + +  S  + N
Sbjct: 75  -LAIGLTGQRLLGVPIIVQASQAEKN 99

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 5e-14
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDV 284
           P+ +  +  T+ V NL       DL+++F  +G +        + T   +   FI F+  
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 285 RAAEAALKSLNRSDIAGKRIKLEPSRP 311
             A  A+  ++        + +E ++P
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKP 87

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 3e-11
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTA 205
            + T+ V N++ +  +++L+ LF  +G I  +Y A      + +GF  IS++    A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           +  +         L++ ++ P  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 8e-14
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 232 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK---RHHKFIEFYDVRAAE 288
           + D    TL V NL   V+   + Q+F   G  K  +          + F+EFY+ R A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 289 AALKSLNRSDIAGKRIKLEPSRPGGARR 316
           AAL ++N   I GK +K+  +    +++
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY---DIRAARTA 205
           +   RTL+V N++ +V +  +  LF Q G  ++     +H       +    + R A  A
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 206 MRALQNKPLRRRKLDIHFSIPKDN 229
           + A+  + +  +++ ++++    +
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSS 88

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 9e-14
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 228 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 287
           D  +       T+    +   ++++ +RQ F  +G++ EIR    ++ + F+ F    +A
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESA 67

Query: 288 EAALKSLNRSDIAGKRIKLEPSRP 311
             A+ S+N + I G  +K    + 
Sbjct: 68  AHAIVSVNGTTIEGHVVKCYWGKE 91

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
            + T++   I S + D  +R  F  +G I  +      +G+  + +    +A  A+ ++ 
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
              +    +  ++     + +
Sbjct: 76  GTTIEGHVVKCYWGKESPDMT 96

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.1 bits (158), Expect = 1e-13
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAARTAM 206
           LF++N+N +  +  L+ +F + G I        +         GF  + Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 207 RALQNKPLRRRKLDIHFSIPKDNPS 231
           + LQ   +   KL++  S     P+
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.9 bits (155), Expect = 3e-13
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEV--------KEIRETPHKRHHKFIEFYDVRAAEAAL 291
           L + NL+ S + E L+ +F   G +        K            F+E+     A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 292 KSLNRSDIAGKRIKLEPSRPG 312
           K L    + G ++++  S   
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 1e-13
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L V  L   V ++ L   F  +G++ +I      ET   R   F+EF     A AA+ +
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 294 LNRSDIAGKRIKLEPSRP 311
           +N S++ G+ I++  ++P
Sbjct: 67  MNESELFGRTIRVNLAKP 84

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 2e-12
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 205
             R L+V  +   V+D  L A F  +GDI  +         KHRGF  + +     A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 206 MRALQNKPLRRRKLDIHFSIPK 227
           +  +    L  R + ++ + P 
Sbjct: 64  IDNMNESELFGRTIRVNLAKPM 85

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.9 bits (158), Expect = 2e-13
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 229 NPSDKDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 287
             +D       + + NL+   V   D+  IF  YG++         +   F+++ + R A
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNA 63

Query: 288 EAALKSLNRSDIAGKRIKLEPSRPGGARRN 317
            AA+   +   IAG+ + +  +      R+
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (143), Expect = 2e-11
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 151 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 209
            +  +F+ N+N+  V+ S++ A+F +YG I        H+GF  + Y + R AR A+   
Sbjct: 14  MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVG---CSVHKGFAFVQYVNERNARAAVAGE 70

Query: 210 QNKPLRRRKLDIHFSIPKDNP 230
             + +  + LDI+ +      
Sbjct: 71  DGRMIAGQVLDINLAAEPKVN 91

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 3e-13
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 154 TLFVRNINSNVEDSELRALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 206
            LF+  I    +  E+     +            +     K+RGF  + Y   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 207 RALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQ 237
           R L    ++    ++ + ++ P+ +  +  +  
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 5e-10
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 9/82 (10%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE-------IRETPHKRHHKFIEFYDVRAAEAAL 291
            L +  +      E++ +      E            +    R   F+E+   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 292 KSLNRSDI--AGKRIKLEPSRP 311
           + L    I   G +I ++ + P
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEP 84

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 4e-13
 Identities = 13/79 (16%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL 294
           L +  L   ++++ ++++  ++G +K         T   + + F E+ D+   + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 295 NRSDIAGKRIKLEPSRPGG 313
           N   +  K++ ++ +  G 
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 4e-10
 Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAM 206
           +  LF+  + + + D +++ L   +G ++             +G+    Y DI     A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 207 RALQNKPLRRRKLDIHFSIPKDNPS 231
             L    L  +KL +  +      +
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAKNA 85

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.4 bits (154), Expect = 5e-13
 Identities = 21/94 (22%), Positives = 45/94 (47%), Gaps = 13/94 (13%)

Query: 225 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE------VKEIRETPHKRHHKF 278
           +PK   + K      ++V N+    +  ++R++F  +GE       K++  T   R   F
Sbjct: 2   VPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 55

Query: 279 IEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP 311
           ++F   + A+ A  +L + + + G+R+ LE +  
Sbjct: 56  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.3 bits (146), Expect = 6e-12
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC------KHRGFVMISYYDIRAA 202
           +  +  + VRNI       E+R LF  +G+++T+           HRGF  + +   + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 203 RTAMRALQN-KPLRRRKLDIHFSIPKD 228
           + A  AL +   L  R+L + ++  + 
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 5e-13
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 293
            L+V  L  +++ E+ R +FG+ GE++  +      T     + F+ + D + AE A+ +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 294 LNRSDIAGKRIKLEPSRP 311
           LN   +  K IK+  +RP
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 152 SRT-LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTA 205
           S+T L V  +  N+   E R+LF   G+I +             G+  ++Y D + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 206 MRALQNKPLRRRKLDIHFSIP 226
           +  L    L+ + + + ++ P
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 1e-12
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 294 LNRSDIAGKRIK 305
            N  ++ G+RI+
Sbjct: 71  ANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 3e-10
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTA 205
           P+  L V  ++    + +LR +F +YG I  +      +      F  + + ++  A+ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 206 MRALQNKPLRRRKLDI 221
                   L  R++ +
Sbjct: 68  KERANGMELDGRRIRV 83

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.5 bits (149), Expect = 2e-12
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVK-----EIRETPHKRHHKFIEFYDVRAAEAALKS 293
            L V NL  +++++ L  IFG YG +        + T   R   F+ +     A+ A+ +
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 294 LNRSDIAGKRIKLE 307
           LN     G    L 
Sbjct: 68  LNNVIPEGGSQPLS 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAM 206
              L+V N+   + D +L  +F +YG I            + RG   + Y     A+ A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 207 RALQNKPL--RRRKLDIHF 223
            AL N       + L +  
Sbjct: 66  SALNNVIPEGGSQPLSVRL 84

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 20/89 (22%), Positives = 46/89 (51%), Gaps = 6/89 (6%)

Query: 151 PSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAART 204
           P+ T+++ N+N  ++  EL+    A+F ++G I    +  + K RG   + + ++ +A  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 205 AMRALQNKPLRRRKLDIHFSIPKDNPSDK 233
           A+R++Q  P   + + I ++    +   K
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 5e-11
 Identities = 16/79 (20%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKE--IRETPHKRHHKFIEFYDVRAAEAALK 292
           T+ + NL+  +  ++L++    IF  +G++ +  +  +   R   F+ F +V +A  AL+
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 293 SLNRSDIAGKRIKLEPSRP 311
           S+       K ++++ ++ 
Sbjct: 65  SMQGFPFYDKPMRIQYAKT 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 211
            + L+VRN+  +  +  +   F             K R +  + + +   A  AM+AL  
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 212 KPLRRRKLDIHFSIPKDNPS 231
           K L    +++  + P D  S
Sbjct: 67  KVLDGSPIEVTLAKPVDKDS 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 2e-11
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L V NL  S S E + + F         R     R + F+ F +   A  A+K+LN   
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 299 IAGKRIKLEPSRP 311
           + G  I++  ++P
Sbjct: 69  LDGSPIEVTLAKP 81

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.1 bits (148), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L V NL P ++ E++R++F  YG+  E+      +   FI       AE A   L+   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELDNMP 68

Query: 299 IAGKRIKLEPSRPGGA 314
           + GK++++  +    +
Sbjct: 69  LRGKQLRVRFACHSAS 84

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.2 bits (143), Expect = 1e-11
 Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 143 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 202
           GE  + +     LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A
Sbjct: 1   GEKTFTQR--SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLA 57

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
             A   L N PLR ++L + F+    + +
Sbjct: 58  EIAKVELDNMPLRGKQLRVRFACHSASLT 86

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 3e-12
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 231 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAA 287
           S+       L V N+     + DLRQ+FG +G++ +   I      +   F+ F +   A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 288 EAALKSLNRSDIAGKRIKLEPSRP 311
           + A + L+ + + G++I++  +  
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATA 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 1e-10
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---HRGFVMISYYDIRAARTAMR 207
             + L V NI     D +LR +F Q+G I  +         +GF  +++ +   A  A  
Sbjct: 10  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 69

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPS 231
            L    +  RK++++ +  +   +
Sbjct: 70  KLHGTVVEGRKIEVNNATARVMTN 93

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 3e-12
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            + V      ++ ++LR+ F  YG+V ++      R   F+ F D + A++         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLI 64

Query: 299 IAGKRIKLEPSRPGGARRN 317
           I G  + +  + P     +
Sbjct: 65  IKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           G   S  +FV     ++ + ELR  F QYGD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 208 ALQNKPLRRRKLDIHFSIPKDNPS 231
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 5e-12
 Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 224 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-----KEIRETPHKRHHKF 278
           ++P +    +      L +  L    + E LR  +  +G++          +   R   F
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           + F  +   +AA+       I G+ ++ + +  
Sbjct: 67  VTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA 98

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTA 205
             R LF+  ++    +  LR  +EQ+G +              RGF  +++  +     A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 206 MRALQNKPLRRRKLDIHFSIPKD 228
           M A +   +  R ++   ++ ++
Sbjct: 79  M-AARPHSIDGRVVEPKRAVARE 100

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 6e-12
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 208
           +F+ N++  +++  L   F  +G I               +G+  I++    A+  A+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 209 LQNKPLRRRKLDIHFSIPKDN 229
           +  + L  R + + ++  KD+
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 9e-12
 Identities = 17/82 (20%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALKS 293
           + + NLDP +  + L   F A+G + +        +T + + + FI F    A++AA+++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 294 LNRSDIAGKRIKLEPSRPGGAR 315
           +N   +  + I +  +    ++
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 59.8 bits (144), Expect = 7e-12
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
           TL + N  PS +  ++R +      V      P  R +      +I+      A   ++ 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 294 LNRSDIAGKRIKLEPSRP 311
           LN   I G  +  + S P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.4 bits (130), Expect = 4e-10
 Identities = 14/79 (17%), Positives = 22/79 (27%), Gaps = 5/79 (6%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMR 207
            TL++ N   +     +R L +    +              R F  I       AR  + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 208 ALQNKPLRRRKLDIHFSIP 226
            L    +    L    S P
Sbjct: 62  KLNGLKIEGYTLVTKVSNP 80

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 59.7 bits (144), Expect = 9e-12
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVK-----EIRETPHKRHHKFIEFYDVRAAEAALKS 293
            L V ++      +++++ F  YGE+K       R T   + +  +E+   + A AA ++
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 294 LNRSDIAGKRIKLEPSRPGG 313
           LN ++I G+ I+++     G
Sbjct: 69  LNGAEIMGQTIQVDWCFVKG 88

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 56.3 bits (135), Expect = 1e-10
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTA 205
               LFV +I+   ++ E++  F  YG+I+ ++          +G+ ++ Y   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 206 MRALQNKPLRRRKLDIHFSIPK 227
             AL    +  + + + +   K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 1e-11
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKS 293
           N   + V NL P +  +D+  +F  YG +++I  +         F+EF D R AE A+  
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 294 LNRSDIAGKRIKLEPSRPGGAR 315
            +  D  G R+++E  R G   
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGT 94

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 5/94 (5%)

Query: 136 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--CKHRGFVM 193
           +G G + G  P G      ++V N+  ++   ++  +F +YG IR +          F  
Sbjct: 1   SGGGVIRG--PAGN-NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF 57

Query: 194 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 227
           + + D R A  A+           +L + F    
Sbjct: 58  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.8 bits (144), Expect = 1e-11
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 13/93 (13%)

Query: 232 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKF 278
           D+D +   + V  L+ SV+ +DL   F   G VK               +ET   +    
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 279 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           + + D   A+AA++  +  D  G ++K+  +R 
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (124), Expect = 6e-09
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 13/95 (13%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-------------CKHRGFV 192
           P  +  +  ++V+ +N +V   +L   F+Q G ++                   K +G  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 227
            +SY D   A+ A+     K  +  KL +  +  K
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 1e-11
 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 9/102 (8%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAM 206
           G+ P   + V N+   V    L  +F ++G + + +     ++   ++ Y D  +A+ A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 207 RALQNKPL--RRRKLDIHFS------IPKDNPSDKDLNQGTL 240
            +L  + +      L I FS      +  +N   +D  +  L
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDL 104

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 7e-11
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 11/96 (11%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRSD 298
           ++V NL   V+ + L QIF  +G V +I       +    +++ D  +A+ A  SL+  +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 299 I--AGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 332
           I  A   ++++ S+           LN +   D+SR
Sbjct: 70  IYNACCTLRIDFSKLT--------SLNVKYNNDKSR 97

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH-----HKFIEFYDVRAAEAALKSL 294
           + +  L    + E LR+ FG +GEVKE                F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 295 NRSDIAGKRIK 305
           +R ++  K I 
Sbjct: 62  SRHELDSKTID 72

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMRAL 209
           +F+  ++       LR  F Q+G+++             RGF  +++ D       + A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 210 QNKPLRRRKLDI 221
               L  + +D 
Sbjct: 62  SRHELDSKTIDP 73

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.2 bits (140), Expect = 4e-11
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALK 292
           G L V NL  + S EDL ++F AYG + E+               F+ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 293 SLNRSDIAGKRIKLEPSRPGGARRN 317
            ++     G+ + + PS        
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 3e-09
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAA 202
           G   S  LFVRN++    + +L  LF  YG +  L+          +GF  +++     A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 231
             A   +  +  + R L +  S  K   S
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 5e-11
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            L+V  L    + +DL++ F  +GEV  +      +T H +   F+ F +       +  
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 294 LNRSDIAGKRIKLEPSRPGGAR 315
            +   I G+    +      ++
Sbjct: 70  RH--MIDGRWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 11/88 (12%), Positives = 26/88 (29%), Gaps = 7/88 (7%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAA 202
               +  L V  +     + +L+  F  +G++  +           +GF  + + +    
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNP 230
              M       +  R  D      K + 
Sbjct: 64  VKVMSQRHM--IDGRWCDCKLPNSKQSQ 89

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALKS 293
            L V  L  +++ ++L Q+F  YG +   R    +         FI F     AE A+K 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 294 LNRSDIAGKRIKLE 307
           LN    +G    + 
Sbjct: 68  LNGQKPSGATEPIT 81

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 8e-10
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 7/79 (8%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 207
             L+V  +   +   EL  LF QYG I T            RG   I +     A  A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 208 ALQNKPL--RRRKLDIHFS 224
            L  +        + + F+
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.3 bits (135), Expect = 9e-11
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 6/71 (8%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 294
           + V  L  + + ED++  F  +G+V +        T   R   F+ F      E   + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 295 NRSDIAGKRIK 305
           +  +I  K ++
Sbjct: 61  HFHEINNKMVE 71

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.8 bits (100), Expect = 5e-06
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRAL 209
           +FV  ++ N    +++  FEQ+G +         T  +HRGF  +++            +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 210 QNKPLRRRKLDI 221
               +  + ++ 
Sbjct: 61  HFHEINNKMVEC 72

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 154 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK- 212
            L++ N++  V   +LR LF                G+  + Y D   A  A+  L  K 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 213 PLRRRKLDIHFSIPKDNPS 231
            L  + +++ +S+ K   S
Sbjct: 62  ELHGKIMEVDYSVSKKLRS 80

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RS 297
            L + NL P+V+ +DLRQ+FG        +    K  + F+++ D   A  A+++L+ + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ-VLLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 298 DIAGKRIKLEPSRPGGAR 315
           ++ GK ++++ S     R
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 293
            L +++L     ++DL Q+F  +G V   +    K+ +      F+ + +  +A+AA++S
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 294 LNRSDIAGKRIKLEPSRPGGARR 316
           +N   I  KR+K++  R     +
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDSK 102

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 9e-09
 Identities = 16/93 (17%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 142 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 196
           AG    G      LF+ ++     D +L  +F  +G++ +            + F  +SY
Sbjct: 9   AGSQKEGP-EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 197 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
            +  +A+ A++++    +  ++L +     K++
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 3e-10
 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 6/103 (5%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIR 200
           P  +   R++FV NI     + +L+ +F + G +            K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 201 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-KDLNQGTLVV 242
            A +AMR L  +    R L +  +  + N  + K L  G  V+
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 2e-09
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYD 283
           +P+  D +  ++ V N+    + E L+ IF   G V   R    +         F E+ D
Sbjct: 1   DPA-VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
              A +A+++LN  + +G+ ++++ +     +  L
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEEL 94

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 56.5 bits (135), Expect = 4e-10
 Identities = 28/128 (21%), Positives = 54/128 (42%), Gaps = 13/128 (10%)

Query: 193 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 252
           ++S YD       ++ LQ +  +         IP    + +      L+V  +  +V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 253 DLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 307
            LRQ+F  YG ++ ++    +         F++F    +A+ A+  LN  +I  KR+K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 308 PSRPGGAR 315
            +  G  R
Sbjct: 118 LAASGHQR 125

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 48.7 bits (115), Expect = 2e-07
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTA 205
             R L V  I + V++ +LR LFE+YG I ++   C         +  + +    +A+ A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 206 MRALQNKPLRRRKLDIHFSIPKD 228
           +  L    +  ++L +  +    
Sbjct: 101 IAGLNGFNILNKRLKVALAASGH 123

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 7e-10
 Identities = 28/104 (26%), Positives = 52/104 (50%), Gaps = 1/104 (0%)

Query: 239 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 297
            L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  LN  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 298 DIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 341
            + GK I++  S+    +     Q +Q L +D      H+   P
Sbjct: 64  KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 107

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 4e-07
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 152 SRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           +  L V N+N   V    L  LF  YGD++ +      +   ++   D   A+ AM  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 211 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT 239
              L  + + I  S  ++    ++  +  
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQEDQ 90

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.3 bits (130), Expect = 8e-10
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           P+  L+V  +  N   + L   F+++G IRT+    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMR 74

Query: 211 NKPLRRRKLDIHFSIPKDNPS 231
             PL      +     K  PS
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPS 95

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            L V  L P+ S   L + F  +G ++ I          +I++  + AA+AA   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 299 IAG--KRIKLEPSRPG 312
           + G  +R++++ ++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 294
           + +  L    + +DL+  F  +GEV +        T   R   F+ F +  + +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 295 NRSDIAGKRIK 305
               + GK I 
Sbjct: 61  KEHKLNGKVID 71

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 10/72 (13%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 209
           +F+  ++ +    +L+  F ++G++            + RGF  + + +  +    M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 210 QNKPLRRRKLDI 221
           +   L  + +D 
Sbjct: 61  KEHKLNGKVIDP 72

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 5/87 (5%)

Query: 236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAA 290
           ++G L V  L    + + L Q+F  YG++ E+       T   R   F+ F ++  A+ A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 291 LKSLNRSDIAGKRIKLEPSRPGGARRN 317
           + ++N   + G++I+++ +      R+
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 152 SRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAM 206
              LFV  ++ +  +  L  +F +YG I            + RGF  +++ +I  A+ AM
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 207 RALQNKPLRRRKLDIHFSIPKDN 229
            A+  K +  R++ +  +    +
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSD 87

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDVRAAEAALKSL 294
           L +  L P  +++DL ++   YG++        + T   + + F++F    AA+ A+ +L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 295 NRSDIAGKRIK 305
             S +  +  K
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 5e-06
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAMRAL 209
           L++R +     D +L  L + YG I         T  K +G+  + +    AA+ A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 210 QNKPLRRRKL 219
           +   ++ +  
Sbjct: 61  KASGVQAQMA 70

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 2e-09
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 6/71 (8%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 294
           + V  L P    E +R+ FG +GEV+ I      + +K     FI F +    +  ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 295 NRSDIAGKRIK 305
              ++   + +
Sbjct: 61  KYHNVGLSKCE 71

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMRAL 209
           +FV  ++ +  + ++R  F  +G++ ++           RGF  I++ +    +  M   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 210 QNKPLRRRKLDI 221
           +   +   K +I
Sbjct: 61  KYHNVGLSKCEI 72

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 3e-09
 Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 229 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYD 283
           + S KD     + V  L    ++  LR+ F  +G+++E      ++  K     F+   D
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 284 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
             AAE A K  N   I G++  +  +  G   R+L
Sbjct: 62  RAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSL 95

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 9e-07
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 145 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDI 199
               +     +FV  +  +  D+ LR  FE +GDI            K RG+  ++  D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 200 RAARTAMRALQNKPLRRRKLDIHFSIPKDNP 230
            AA  A +   N  +  RK +++ +     P
Sbjct: 63  AAAERACKDP-NPIIDGRKANVNLAYLGAKP 92

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 3e-09
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 6/90 (6%)

Query: 148 GEHPSRTLFVRNINSNVEDS-----ELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 202
           G   S  L     N +V        +  +LF  Y    T +   K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT-FQYFKSFKRVRINFSNPLSA 59

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKDNPSD 232
             A   L       +++ ++F+      S 
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 239 TLVVFNLDPSVSNE-----DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 293
            L+    +  V +E         +F  Y +    +     +    I F +  +A  A   
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRV-RINFSNPLSAADARLR 65

Query: 294 LNRSDIAGKRIKLEPSRP 311
           L++++  GK +KL  ++ 
Sbjct: 66  LHKTEFLGKEMKLYFAQT 83

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (124), Expect = 5e-09
 Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 12/93 (12%)

Query: 230 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 284
           PSD      T+ + NL      E L ++   +G++K +      +T H +   F +F   
Sbjct: 2   PSDVT-EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 285 RAAEAALKSLNRS------DIAGKRIKLEPSRP 311
            AA+  L + +         + G+++K++ +  
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.2 bits (119), Expect = 2e-08
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIR 200
           P      +T+F+RN++ + E+  L  + +Q+GD++ +           +G     +    
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 201 AARTAMRALQ------NKPLRRRKLDIHFSIPKDNPS 231
           AA+  + A           L  R+L +  ++ +D  +
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 7e-09
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR-----TA 205
           P++ L+++N++  V + +L +LF ++ + +      +     M     I          A
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 76

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPS 231
           +  +    L  + L I F   K   S
Sbjct: 77  LHLVNGYKLYGKILVIEFGKNKKQRS 102

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 2e-08
 Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 9/94 (9%)

Query: 227 KDNPSDKDLNQG----TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHK 277
           +  P     N G     L + NL P V+  DL  +F  + E K         T   R   
Sbjct: 4   RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 63

Query: 278 FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 311
           FI F +   A  AL  +N   + GK + +E  + 
Sbjct: 64  FITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 8e-09
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDVRAAEAALKS 293
            L +  L    ++E LR  F  +G + +        T   R   F+ +  V   +AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 294 LNRSDIAGKRIK 305
                + G+ ++
Sbjct: 67  ARPHKVDGRVVE 78

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 7e-07
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 207
           R LF+  ++    D  LR+ FEQ+G +              RGF  ++Y  +     AM 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 208 ALQNKPLRRRKLDI 221
           A +   +  R ++ 
Sbjct: 67  A-RPHKVDGRVVEP 79

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.3 bits (122), Expect = 1e-08
 Identities = 16/100 (16%), Positives = 42/100 (42%), Gaps = 4/100 (4%)

Query: 137 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 196
           G+   +G H      S  + VR +  +V +++L    E++G I  +      +   ++ +
Sbjct: 1   GSSGSSGSHHKVS-VSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEF 58

Query: 197 YDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKD 234
            +I +A+  +    + P  +  ++   ++S  K      +
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGN 98

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 4e-06
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            + V  L  SV   DL +    +G +  +      +    +EF ++ +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 299 --IAGKRIKLEPSRPGGARR 316
             IAG++     S      R
Sbjct: 76  VYIAGQQAFFNYSTSKRITR 95

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 11/80 (13%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           G   S  + V+N+  +    E+  L + Y          +++    ++  +   A+ A++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 208 ALQNKPLRRRKLDIHFSIPK 227
                  R + L +      
Sbjct: 59  MFHQYSFRGKDLIVQLQPTD 78

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 9/73 (12%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            ++V NL    + +++  +   Y            +   F+   +   A+ A++  ++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLK--YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 299 IAGKRIKLEPSRP 311
             GK + ++    
Sbjct: 65  FRGKDLIVQLQPT 77

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRS 297
           TL + N+ PSVS EDL+ +F + G V +  +     R    I+   V  A  AL  L+  
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 71

Query: 298 DIA-GKRIKLEPSRP 311
           D+     +++  S+ 
Sbjct: 72  DLGENHHLRVSFSKS 86

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 2e-07
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAMRAL 209
           PS TL + NI  +V + +L+ LF   G + +      K R   +I    +  A  A+  L
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 210 QNKPLRR-RKLDIHFS 224
            N  L     L + FS
Sbjct: 69  HNHDLGENHHLRVSFS 84

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.4 bits (117), Expect = 3e-08
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 239 TLVVFNLDPSVSNED-LRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEAAL 291
            +++ NL   + +E+ LR+ F  +G +++I      +E        F+ F +  +AE AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 292 KSLNRSDIAGKRIKLEPSRP 311
           + +NRS +  + I +  +  
Sbjct: 66  Q-MNRSLLGNREISVSLADK 84

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 152 SRTLFVRNINSNV-EDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAART 204
            R + +RN+++ + +++ LR  FE +G I  +           +     + + +  +A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 205 AMRALQNKPLRRRKLDIHFSIPK 227
           A+  +    L  R++ +  +  K
Sbjct: 64  AL-QMNRSLLGNREISVSLADKK 85

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 4e-08
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
           TL V+  D  ++   LR  F  +G + ++      R+  F+ +  + +A+ A+  LN + 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLS-MDPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 299 IAGKRIKLEPSRP 311
           +   ++K+  +R 
Sbjct: 64  VESVQLKVNIARK 76

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 9e-08
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
              TL+V   +  +  + LR  F  +G+I  L           ++Y  + +A  A+  L 
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELN 60

Query: 211 NKPLRRRKLDIHFSIPK 227
              +   +L ++ +  +
Sbjct: 61  GTQVESVQLKVNIARKQ 77

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 7e-08
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 4/83 (4%)

Query: 233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE----VKEIRETPHKRHHKFIEFYDVRAAE 288
           ++ +   L + NL  S+  ++L  +   +G+          +   R   F         E
Sbjct: 14  QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 73

Query: 289 AALKSLNRSDIAGKRIKLEPSRP 311
           A +   N   I        P+ P
Sbjct: 74  AVIGHFNGKFIKTPPGVSAPTEP 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 9e-07
 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 4/82 (4%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGD----IRTLYTACKHRGFVMISYYDIRAART 204
           E     L++ N+  ++++ EL  + + +G          ++   RG              
Sbjct: 15  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 205 AMRALQNKPLRRRKLDIHFSIP 226
            +     K ++        + P
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTEP 96

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.5 bits (115), Expect = 7e-08
 Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 151 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 209
             R + + +         +L  L E +G I              I       A+ A+   
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYY 65

Query: 210 QNKP--LRRRKLDIHFS 224
              P  +  + + +H S
Sbjct: 66  TTTPALVFGKPVRVHLS 82

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 239 TLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLN 295
            + + +          L Q+   +G +       +K +  FIE      A+AA+   +  
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL-ILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 296 RSDIAGKRIKLEPSRP 311
            + + GK +++  S+ 
Sbjct: 69  PALVFGKPVRVHLSQK 84

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGE-----VKEIRETPHKRHHKFIEFYDVRAAEAALKS 293
           T  + NL   V+ E +++ F           +E       +   + EF D+ +  +AL  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 294 LNRSDIAGKRIKLEPSRPGGARR 316
           LN   +  KRI+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 13/86 (15%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 205
           P  T F+ N+  +V +  ++  F           R      + +GF    + D+ +  +A
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 206 MRALQNKPLRRRKLDIHFSIPKDNPS 231
           + +L  + L  +++ +  +    +  
Sbjct: 74  L-SLNEESLGNKRIRVDVADQAQDKD 98

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
                   E   ++   YGEV+E+        H   + +++F     AE A+  LN    
Sbjct: 34  EHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF 93

Query: 300 AGKRIKLEPS 309
            G+ I  E S
Sbjct: 94  NGQPIHAELS 103

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 9e-05
 Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMRALQ 210
           + ++       +     + E+YG++  +             V + +     A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 211 NKPLRRRKLDIHFS 224
           N+    + +    S
Sbjct: 90  NRWFNGQPIHAELS 103

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 47.5 bits (112), Expect = 1e-07
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           P++ LF+ N+     +  L  LF Q+   + +           + +     +  A  ALQ
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQ 66

Query: 211 NKPL-RRRKLDIHFS 224
              +     + I F+
Sbjct: 67  GFKITPTHAMKITFA 81

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 252 EDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 310
           EDLR     +G+++++     H      + F D   A+  +++L+     G++I  +   
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

Query: 311 P 311
            
Sbjct: 94  G 94

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 9e-06
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 12/91 (13%)

Query: 151 PSRTLFVRNI--NSNVEDS---------ELRALFEQYGDIRTLYTACKH-RGFVMISYYD 198
             R + ++N+    + ED          +LR    ++G IR L    +H  G   +S+ D
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD 66

Query: 199 IRAARTAMRALQNKPLRRRKLDIHFSIPKDN 229
              A   ++ L  +    R++         +
Sbjct: 67  PEEADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 2e-07
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            + V  +        LR  F  YG+++ I     R +  KR   F+ F D  + +  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 294 LNRSDIAGKRIK 305
                + G   +
Sbjct: 63  QKYHTVNGHNCE 74

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 4/77 (5%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY----YDIRAARTAMRA 208
           + +FV  I  + E+  LR  FEQYG I  +             +    +D   +   +  
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 209 LQNKPLRRRKLDIHFSI 225
            +   +     ++  ++
Sbjct: 63  QKYHTVNGHNCEVRKAL 79

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 2e-07
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
           PSR L +R +   V ++E+ AL   +G +       K +    +      AA T +    
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPFGKVTN-ILMLKGKNQAFLELATEEAAITMVNYYS 65

Query: 211 NKP--LRRRKLDIHFSIPK 227
                LR + + I +S  K
Sbjct: 66  AVTPHLRNQPIYIQYSNHK 84

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 4e-07
 Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 150 HPSRTLFVR--NINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 207
           + +++L V    + + V  ++L  + E+ G +  L     ++ +    Y     ++ A  
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYV 74

Query: 208 ALQNKPL---RRRKLDIHFS 224
            L  K +     +K+ ++ +
Sbjct: 75  TLNGKEVVDDLGQKITLYLN 94

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 4e-07
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 239 TLVVF--NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           +LVV    L   VS   L  +    G V  +   P  + + F  +     ++ A  +LN 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-MPPNKPYSFARYRTTEESKRAYVTLNG 78

Query: 297 SDI---AGKRIKLEPS 309
            ++    G++I L  +
Sbjct: 79  KEVVDDLGQKITLYLN 94

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 7e-07
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 13/87 (14%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----------ETPHKRHHKFIEFYDVRAAE 288
            L V N+   ++ E +   F A   +  +           +    ++  F+EF  V    
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 289 AALKSLNRSDIAGKRIKLEPSRPGGAR 315
            A+   +     G+ +K+   RP   +
Sbjct: 63  QAMA-FDGIIFQGQSLKI--RRPHDYQ 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 8e-06
 Identities = 14/86 (16%), Positives = 26/86 (30%), Gaps = 13/86 (15%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTL----------YTACKHRGFVMISYYDIRAA 202
           R L+V NI   + +  +   F     +  L              + + F  + +  +   
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 203 RTAMRALQNKPLRRRKLDIHFSIPKD 228
             AM        + + L I    P D
Sbjct: 62  TQAMA-FDGIIFQGQSLKI--RRPHD 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 2e-06
 Identities = 16/102 (15%), Positives = 34/102 (33%), Gaps = 3/102 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
                +LD     EDL  +F  +GE+K I      +    +     + A    K  N  +
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 299 IAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGS 340
           +  +  ++      G       +  +++ +D+   L      
Sbjct: 73  LQLRNKEVTWEVLEGEVEK---EALKKIIEDQQESLNKWKSK 111

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 4e-06
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD-IRAARTAMRALQN 211
              F  +++      +L  LF  +G+I+ +          +I + +  + A    +   N
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANN 70

Query: 212 KPLRRRKLDIHFSIPKD 228
             L+ R  ++ + + + 
Sbjct: 71  GNLQLRNKEVTWEVLEG 87

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 3e-06
 Identities = 8/81 (9%), Positives = 27/81 (33%), Gaps = 5/81 (6%)

Query: 233 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAE 288
            D+   ++ +       + +D+++     G+V  I+             F+ F  + +A+
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 289 AALKSLNRSDIAGKRIKLEPS 309
             ++           + +   
Sbjct: 62  KFVE-TPGQKYKETDLLILFK 81

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 7e-06
 Identities = 8/80 (10%), Positives = 30/80 (37%), Gaps = 5/80 (6%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAART 204
           +  +R+++++   ++    +++   E  G +  +             + + +  I +A+ 
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 205 AMRALQNKPLRRRKLDIHFS 224
            +     +  +   L I F 
Sbjct: 63  FV-ETPGQKYKETDLLILFK 81

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 5e-06
 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 2/82 (2%)

Query: 146 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 205
           P        + V  +  +    +L+    + GD+          G V            A
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYL--RKEDMEYA 66

Query: 206 MRALQNKPLRRRKLDIHFSIPK 227
           +R L +   R  + +  +    
Sbjct: 67  LRKLDDTKFRSHEGETSYIRVY 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 298
            ++V  L PS S +DL+      G+V        K     +E+      E AL+ L+ + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVCYAD--VQKDGMGMVEYLRKEDMEYALRKLDDTK 74

Query: 299 IAGKRIKLEPSRPGGARRN 317
                 +    R    R +
Sbjct: 75  FRSHEGETSYIRVYPERSS 93

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 293
            + V N+  +VS +++   F  Y  +         E         + F     A AA+  
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 294 LNRSDIAGKRIKLE 307
           LN   I  +++KL 
Sbjct: 71  LNDRPIGSRKVKLV 84

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAA 202
           G+     + V+N+   V   E+   F  Y  I        +      G  M+++     A
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 203 RTAMRALQNKPLRRRKLDI 221
             A+  L ++P+  RK+ +
Sbjct: 65  TAAVIDLNDRPIGSRKVKL 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 2/75 (2%)

Query: 649 SGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP 708
           SG+   T + ++N+P   +   +L                    +     G A +   S 
Sbjct: 4   SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV--CLKYNEKGMPTGEAMVAFESR 61

Query: 709 LHIIPFYEAFNGKKW 723
                     N +  
Sbjct: 62  DEATAAVIDLNDRPI 76

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 42.2 bits (98), Expect = 1e-05
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAM 206
               LF+ N+N N   +EL+    +      L       G    F  + +        A+
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71

Query: 207 RALQNKPLRRRKLDIHFSIPK 227
             L    +   ++ +     +
Sbjct: 72  E-LTGLKVFGNEIKLEKPKGR 91

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 237 QGTLV-VFNLDPSVSNEDLRQI------FGAYGEVKEIRETPHKRHHKF-----IEFYDV 284
           Q  LV V  L   +++ ++ +       FG   +V     T +           + +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 285 RAAEAALKSLNRSDIAGKRIK 305
             A  A++ +N   + G+ +K
Sbjct: 67  EDALRAIQCVNNVVVDGRTLK 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 0.002
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 153 RTLFVRNINSNVEDSELRALFE---QYGDI--------RTLYTACKHRGFVMISYYDIRA 201
             +FV  ++  + D E+    E   ++G I         +   +        ++Y     
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 202 ARTAMRALQNKPLRRRKL 219
           A  A++ + N  +  R L
Sbjct: 69  ALRAIQCVNNVVVDGRTL 86

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 4e-05
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 2/78 (2%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           +VV  L PS S +DL+                ++     +EF        A++ L+ +  
Sbjct: 3   VVVSGLPPSGSWQDLKDHM--REAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 60

Query: 300 AGKRIKLEPSRPGGARRN 317
                +    R       
Sbjct: 61  RSHEGETAYIRVKVDGPR 78

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 6e-05
 Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 17/95 (17%)

Query: 151 PSRTLFVRNI------NSNVEDSELR-ALFEQYGDIRTLYTACKHR----------GFVM 193
           P+  L + N+        + E  E+   + ++      + +    R          G + 
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 194 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 228
           + +  +   + AM+ L  +    R +   +  P  
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 7/75 (9%)

Query: 244 NLDPSVSNEDLRQIFGAYGEVKEIR-------ETPHKRHHKFIEFYDVRAAEAALKSLNR 296
           + +     ED+R     YG VK I                 F+EF  V   + A++ L  
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 297 SDIAGKRIKLEPSRP 311
              A + +  +   P
Sbjct: 81  RKFANRVVVTKYCDP 95

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (86), Expect = 4e-04
 Identities = 10/68 (14%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 299
           +++  L   V+N+++  +   Y    +       +   F+   +   AEAA+ + ++S +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY--ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 300 AGKRIKLE 307
             + + ++
Sbjct: 59  RERELSVQ 66

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.4 bits (83), Expect = 0.001
 Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 214
           + +R +  +V + E+  L   Y          K   FV     +   A  A+       L
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVT--LLNGEQAEAAINTFHQSRL 58

Query: 215 RRRKLDIHFSIPKD 228
           R R+L +    P D
Sbjct: 59  RERELSVQLQ-PTD 71

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.4 bits (88), Expect = 5e-04
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 210
               +  +N+ +    +E++  F ++G +  +          ++ + +   AR A R L 
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLA 67

Query: 211 NKPLRRRKLDIHFS---IPKDNPSDKD 234
                   L + ++   +    P  KD
Sbjct: 68  YSKFHHVPLYLEWAPIGVFGAAPQKKD 94

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 7e-04
 Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 6/97 (6%)

Query: 227 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEF 281
           +            + +  L     N+ +   F     V++     +  + K     F+EF
Sbjct: 8   RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 67

Query: 282 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 318
            +    +AAL   ++  +  + I++ P    G    +
Sbjct: 68  RNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKI 103

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.9 bits (84), Expect = 0.001
 Identities = 8/83 (9%), Positives = 20/83 (24%), Gaps = 2/83 (2%)

Query: 149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 208
           +   R + + N+  +           +       Y   + +    I       A   +  
Sbjct: 15  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDH 74

Query: 209 LQNKP--LRRRKLDIHFSIPKDN 229
              K    + R + +  S     
Sbjct: 75  CLKKALWFQGRCVKVDLSEKYKK 97

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 655 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNV-GYAFINMLSPLHIIP 713
           + ++I+ +P   T + L   +    +  Y F +   D     ++   A+IN  +   II 
Sbjct: 2   SKVVIRRLPPTLTKEQLQEHLQPMPEHDY-FEFFSNDTSLYPHMYARAYINFKNQEDIIL 60

Query: 714 FYEAFNGKKWE-KFNSEKVASLAYA 737
           F + F+G  +      E  A + +A
Sbjct: 61  FRDRFDGYVFLDNKGQEYPAIVEFA 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	818
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.92
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.62
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.61
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.61
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.6
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.6
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.6
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.6
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.59
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.59
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.59
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.59
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.59
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.59
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.58
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.58
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.58
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.58
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.58
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.57
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.57
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.57
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.57
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.56
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.56
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.56
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.56
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.55
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.55
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.55
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.55
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.55
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.55
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.55
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.55
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.54
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.54
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.54
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.54
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.53
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.53
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.53
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.53
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.53
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.53
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.53
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.53
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.53
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.53
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.53
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.53
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.53
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.53
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.52
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.52
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.52
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.52
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.51
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.51
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.51
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.51
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.51
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.5
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.5
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.5
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.5
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.5
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.5
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.49
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.49
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.49
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.49
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.49
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.48
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.48
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.48
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.48
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.48
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.48
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.48
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.48
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.47
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.47
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.47
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.47
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.47
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.47
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.47
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.47
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.46
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.46
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.46
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.45
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.45
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.45
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.45
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.45
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.44
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.44
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.44
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.44
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.43
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.43
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.43
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.43
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.43
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.42
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.42
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.42
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.42
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.42
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.41
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.41
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.4
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.39
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.38
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.37
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.37
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.36
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.36
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.36
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.36
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.35
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.34
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.3
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.29
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.25
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.18
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.18
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.18
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.16
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.16
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.11
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.11
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.1
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.05
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.05
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.93
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.88
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.82
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.76
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.98
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.43
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.54
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.28
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	94.78
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	89.46
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	81.76

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=2.7e-25  Score=219.47  Aligned_cols=162  Identities=19%  Similarity=0.375  Sum_probs=138.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .|+|||+|||+++|+++|+++|++||.|..+.+     +++++|||||+|.+.++|++|+. +.+..+.++.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            489999999999999999999999999998873     57889999999999999999999 466677777777766544


Q ss_pred             CCCC--CCCCCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCcc
Q 003463          227 KDNP--SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI  299 (818)
Q Consensus       227 k~~~--~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i  299 (818)
                      +...  .......++|||+|||..+|+++|+++|+.||.|..+.+     ++.++|||||+|.+.++|.+|++ +++..+
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~  163 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTV  163 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEE
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeE
Confidence            3321  123345579999999999999999999999999999864     35678999999999999999997 799999


Q ss_pred             CCceEEEEecCCCccc
Q 003463          300 AGKRIKLEPSRPGGAR  315 (818)
Q Consensus       300 ~Gr~L~V~~a~~~~~r  315 (818)
                      .|++|+|.+|.++.++
T Consensus       164 ~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         164 NGHNCEVRKALSKQEM  179 (183)
T ss_dssp             TTEEEEEEECCCHHHH
T ss_pred             CCEEEEEEecCCcccc
Confidence            9999999999887543

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-18  Score=171.49  Aligned_cols=154  Identities=18%  Similarity=0.284  Sum_probs=124.0

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeecCCCCCcccEEEEEecChhhcc---ccCccccCCCCc-------c
Q 003463           74 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAG-------T  140 (818)
Q Consensus        74 ~~e~~V~~Lp~s~~E~el~diF~~~G~i---~V~~d~~t~~skG~a~v~f~~~~~a~---~~~~~~l~n~~~-------~  140 (818)
                      ++++||++||..+++.+++++|+.+|.|   .+..+..++.++|++|+.|.+.+.+.   ......+.....       .
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            4679999999999999999999999987   46778889999999999999887554   221111111110       1


Q ss_pred             ccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          141 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       141 ~~g~~~~~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                      ............++|||+|||.++|+++|+++|+.||.|..+.+     +++++|||||+|.+.++|++|++ +++..+.
T Consensus        86 ~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~  164 (183)
T d1u1qa_          86 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN  164 (183)
T ss_dssp             TGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET
T ss_pred             ccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC
Confidence            11112234456789999999999999999999999999999873     46789999999999999999997 7889999


Q ss_pred             cccccccccCCCC
Q 003463          216 RRKLDIHFSIPKD  228 (818)
Q Consensus       216 gr~L~V~~a~pk~  228 (818)
                      |++|+|.++.++.
T Consensus       165 G~~i~V~~A~~k~  177 (183)
T d1u1qa_         165 GHNCEVRKALSKQ  177 (183)
T ss_dssp             TEEEEEEECCCHH
T ss_pred             CEEEEEEecCCcc
Confidence            9999999987753

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.64  E-value=2.2e-16  Score=135.59  Aligned_cols=76  Identities=28%  Similarity=0.436  Sum_probs=70.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..+|||+|||+++|+++|+++|++||.|+++++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+||+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            357999999999999999999999999999975     455689999999999999999999999999999999999988


Q ss_pred             C
Q 003463          312 G  312 (818)
Q Consensus       312 ~  312 (818)
                      +
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.6e-16  Score=136.19  Aligned_cols=78  Identities=22%  Similarity=0.357  Sum_probs=72.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+||+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4578999999999999999999999999999975     45678899999999999999999999999999999999999


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      |+.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.9e-16  Score=133.25  Aligned_cols=74  Identities=30%  Similarity=0.515  Sum_probs=69.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      .+|||+|||.++++++|+++|++||.|.+|++     .+..+|||||+|.+.++|++|++.|||..+.|++|+|+||+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            47999999999999999999999999999975     346678999999999999999999999999999999999987

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1e-15  Score=134.97  Aligned_cols=78  Identities=26%  Similarity=0.330  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||..+|+++|+++|++||.|.++++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++|+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            3468999999999999999999999999999975     46788999999999999999999999999999999999998


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            875

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.61  E-value=5.6e-16  Score=133.00  Aligned_cols=75  Identities=23%  Similarity=0.450  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      +++|||+|||.++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            578999999999999999999999999999883     567899999999999999999999999999999999999976

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=5.6e-16  Score=135.38  Aligned_cols=80  Identities=26%  Similarity=0.454  Sum_probs=73.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            3468999999999999999999999999999975     46779999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003463          311 PGGAR  315 (818)
Q Consensus       311 ~~~~r  315 (818)
                      |+..+
T Consensus        84 p~~~k   88 (89)
T d2cqba1          84 PMRIK   88 (89)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            86543

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.60  E-value=7e-16  Score=134.51  Aligned_cols=78  Identities=24%  Similarity=0.385  Sum_probs=71.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            4568999999999999999999999999999875     35568999999999999999999999999999999999998


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      +++
T Consensus        86 ~kG   88 (88)
T d1rk8a_          86 VKG   88 (88)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            764

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.1e-15  Score=134.58  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=73.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|.+|++.|||..+.|++|+|+|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4569999999999999999999999999999975     45568899999999999999999999999999999999998


Q ss_pred             CCcccc
Q 003463          311 PGGARR  316 (818)
Q Consensus       311 ~~~~r~  316 (818)
                      .....+
T Consensus        86 ~~~~gr   91 (93)
T d1h2vz_          86 GFKEGR   91 (93)
T ss_dssp             CCCTTC
T ss_pred             CCCCCC
Confidence            765444

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.6e-15  Score=132.71  Aligned_cols=81  Identities=30%  Similarity=0.383  Sum_probs=73.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...++|||+|||.++|+++|+++|++||.|.+|++.   ...++||||+|.+.++|.+|++.|+|..+.|+.|+|.||++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            345699999999999999999999999999999762   34578999999999999999999999999999999999988


Q ss_pred             Cccc
Q 003463          312 GGAR  315 (818)
Q Consensus       312 ~~~r  315 (818)
                      +..+
T Consensus        86 ~~~~   89 (90)
T d2cqia1          86 PSSQ   89 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7654

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=2e-15  Score=133.32  Aligned_cols=78  Identities=24%  Similarity=0.477  Sum_probs=72.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe------cCCCCceEEEEEcCHHHHHHHHHHc-CCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~L-nG~~i~Gr~L~V~~  308 (818)
                      ...+|||+|||.++++++|+++|++||.|..|++      ++.++|||||+|.+.++|.+|++.| ||..+.|++|+|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            4568999999999999999999999999999976      3567899999999999999999998 89999999999999


Q ss_pred             cCCCc
Q 003463          309 SRPGG  313 (818)
Q Consensus       309 a~~~~  313 (818)
                      |++..
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98765

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.6e-15  Score=133.62  Aligned_cols=79  Identities=16%  Similarity=0.324  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|+++
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44689999999999999999999999999999973     5789999999999999999999999999999999999999


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8765

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=9.6e-16  Score=131.40  Aligned_cols=75  Identities=23%  Similarity=0.478  Sum_probs=70.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .++|||+|||.++++++|+++|++||+|..|++     .++++|||||+|.+.++|++|++.|+|..+.|++|+|.|++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            468999999999999999999999999999873     467899999999999999999999999999999999999976

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=2.1e-15  Score=137.44  Aligned_cols=99  Identities=21%  Similarity=0.421  Sum_probs=82.8

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      .++|||+|||..+|+++|+++|++||.|++|++  ++..+|||||+|.+.++|.+|++.|||..|.|+.|+|.++.+...
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~   86 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRA   86 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCch
Confidence            468999999999999999999999999999986  456789999999999999999999999999999999999875432


Q ss_pred             cchhhhccchhccHHHHHHHHhhcC
Q 003463          315 RRNLMLQLNQELEQDESRILQHQVG  339 (818)
Q Consensus       315 r~~~~~ql~~~~~~~~l~~~f~~~G  339 (818)
                      .    ........++.+.....++|
T Consensus        87 ~----~~~~~~~~~~~~~~~~~~~g  107 (114)
T d2f9da1          87 F----QKMDTKKKEEQLKLLKEKYG  107 (114)
T ss_dssp             T----TTSCHHHHHHHHHHHHHHHC
T ss_pred             h----hhhHHHHHHHHHHHHHHHhC
Confidence            2    22333344566667777777

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.1e-15  Score=133.86  Aligned_cols=80  Identities=21%  Similarity=0.453  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            346789999999999999999999999999999873     567899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003463          224 SIPKD  228 (818)
Q Consensus       224 a~pk~  228 (818)
                      +.|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98864

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.59  E-value=1.1e-15  Score=133.22  Aligned_cols=79  Identities=20%  Similarity=0.429  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ....++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345789999999999999999999999999999873     467899999999999999999999999999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9765

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.4e-15  Score=136.39  Aligned_cols=80  Identities=25%  Similarity=0.432  Sum_probs=73.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||+++++++|+++|++||.|.++++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|+|++
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            4568999999999999999999999999998864     45678999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003463          311 PGGAR  315 (818)
Q Consensus       311 ~~~~r  315 (818)
                      ++..+
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            98765

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=9.3e-16  Score=133.96  Aligned_cols=79  Identities=23%  Similarity=0.386  Sum_probs=72.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEec---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      .++|||+|||+++|+++|+++|++||.|..+++.   ..++|||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            4579999999999999999999999999999763   3357999999999999999999999999999999999999876


Q ss_pred             cc
Q 003463          314 AR  315 (818)
Q Consensus       314 ~r  315 (818)
                      +|
T Consensus        88 ~R   89 (89)
T d1cvja2          88 ER   89 (89)
T ss_dssp             TC
T ss_pred             CC
Confidence            43

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.58  E-value=2.7e-15  Score=129.23  Aligned_cols=76  Identities=22%  Similarity=0.332  Sum_probs=71.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC-CceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~-Gr~L~V~~a~  310 (818)
                      ...++|||+|||..+|+++|+++|++||.|++|++...++|||||+|.+.++|.+|++.|+|..+. |++|+|+||+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            345799999999999999999999999999999998778899999999999999999999999885 6899999997

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=3.8e-15  Score=131.15  Aligned_cols=80  Identities=21%  Similarity=0.387  Sum_probs=72.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEec---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      .....+|||+|||+++++++|+++|++||.|++|++.   ..++|||||+|.+.++|.+|++.|||..+.|++|+|++|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            3445689999999999999999999999999999763   3468999999999999999999999999999999999999


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            865

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.58  E-value=9e-16  Score=135.96  Aligned_cols=82  Identities=22%  Similarity=0.366  Sum_probs=76.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ...++|||+|||.++|++||+++|++||.|..++.++.+++||||+|.+.++|++|++.|||..|.|++|+|.|+.++..
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            34579999999999999999999999999999998888999999999999999999999999999999999999998876


Q ss_pred             cc
Q 003463          315 RR  316 (818)
Q Consensus       315 r~  316 (818)
                      ++
T Consensus        94 ~r   95 (96)
T d1fjca_          94 TR   95 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=7.8e-16  Score=134.45  Aligned_cols=78  Identities=27%  Similarity=0.500  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .+++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4689999999999999999999999999999883     57889999999999999999999999999999999999998


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=2.3e-15  Score=128.20  Aligned_cols=73  Identities=25%  Similarity=0.395  Sum_probs=68.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ++|||+|||+++++++|+++|++||.|.++++    +++++|||||+|.+.++|.+|++.|||..+.|++|+|+++.
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            36999999999999999999999999999976    45678899999999999999999999999999999999985

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.8e-15  Score=132.23  Aligned_cols=81  Identities=25%  Similarity=0.519  Sum_probs=73.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+++|+++|+++|++||.|..+.+     ++.++|||||+|.+.++|++|++.|+|..+.|++|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            3467999999999999999999999999999853     45678999999999999999999999999999999999998


Q ss_pred             CCcccc
Q 003463          311 PGGARR  316 (818)
Q Consensus       311 ~~~~r~  316 (818)
                      ++..++
T Consensus        84 ~~~~~r   89 (90)
T d1x5sa1          84 KSSDNR   89 (90)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=3.6e-15  Score=132.67  Aligned_cols=81  Identities=26%  Similarity=0.399  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45788999999999999999999999999999984     5778999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003463          225 IPKDNP  230 (818)
Q Consensus       225 ~pk~~~  230 (818)
                      .++...
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            876644

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=3.5e-15  Score=131.65  Aligned_cols=79  Identities=27%  Similarity=0.519  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEEccHHHHHHHHHHh-cCccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIH  222 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~d~e~A~~Al~~L-ng~~l~gr~L~V~  222 (818)
                      .++++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.| ++..+.|++|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            46789999999999999999999999999999984      4678999999999999999999998 8899999999999


Q ss_pred             ccCCCC
Q 003463          223 FSIPKD  228 (818)
Q Consensus       223 ~a~pk~  228 (818)
                      |+.++.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998654

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.8e-15  Score=129.50  Aligned_cols=73  Identities=29%  Similarity=0.375  Sum_probs=68.2

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      +|||+|||+.+|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|.+|++.|+|..+.|++|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            6999999999999999999999999999975     356689999999999999999999999999999999999863

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.5e-15  Score=132.32  Aligned_cols=79  Identities=25%  Similarity=0.428  Sum_probs=73.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+++|||+|||.++|+++|+++|++||+|.+|.+     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            46789999999999999999999999999999983     5678999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003463          225 IPKD  228 (818)
Q Consensus       225 ~pk~  228 (818)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.5e-15  Score=138.46  Aligned_cols=102  Identities=25%  Similarity=0.399  Sum_probs=85.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ..+++|||+|||.++++++|+++|++||.|..|++  +++++|||||+|.+.++|+.|++.|+|..|.|+.|.|.++.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            35789999999999999999999999999999984  5678999999999999999999999999999999999998643


Q ss_pred             CCCCCCCCCccceeeecCCCCCCHHHHHHHhhccCC
Q 003463          228 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE  263 (818)
Q Consensus       228 ~~~~~~~~~~~tL~V~NLp~~vteedL~~lFs~fG~  263 (818)
                      ....            .......++++..+.++||.
T Consensus        85 ~~~~------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          85 RAFQ------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHTT------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             chhh------------hhHHHHHHHHHHHHHHHhCC
Confidence            2111            11222356788888888874

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.57  E-value=1.7e-15  Score=129.68  Aligned_cols=74  Identities=22%  Similarity=0.287  Sum_probs=66.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      +||||+|||+++|+++|+++|++||.|..+.+     .+.++|||||+|.+.++|.+|++.|||..+.|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            58999999999999999999999999976643     466789999999999999999999999999999999999987

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=5e-15  Score=131.75  Aligned_cols=79  Identities=28%  Similarity=0.415  Sum_probs=72.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||+.+++++|+++|++||.|.+|++     ++.++|||||+|.+.++|.+|++.|||..|.|++|+|.+++
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3567999999999999999999999999999975     45678999999999999999999999999999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ++..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            7653

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=9.2e-16  Score=138.56  Aligned_cols=77  Identities=29%  Similarity=0.517  Sum_probs=71.3

Q ss_pred             ccceeeecCCC-CCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~-~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+||++ .+|+++|+++|++||.|+.|++...++|+|||+|.+.++|.+|++.|||..|.|++|+|+|++...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            35899999965 599999999999999999999887889999999999999999999999999999999999987543

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=2.7e-15  Score=129.99  Aligned_cols=75  Identities=17%  Similarity=0.402  Sum_probs=70.6

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      +|||+|||..+|+++|+++|++||+|.++++     ++.++|||||+|.+.++|.+|++.|||..+.|++|+|++|.++.
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            6999999999999999999999999999975     46779999999999999999999999999999999999998764

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.56  E-value=5.2e-15  Score=127.42  Aligned_cols=78  Identities=18%  Similarity=0.344  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccc-cccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~-gr~L~V~~a~  225 (818)
                      ...|+++|||+|||.++++++|+++|++||+|..|++....+|||||+|.+.++|+.|++.|+|..|. |++|+|.|++
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            34578999999999999999999999999999999987778899999999999999999999999884 6899999985

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.3e-15  Score=131.67  Aligned_cols=76  Identities=24%  Similarity=0.389  Sum_probs=71.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+|||..+++++|+++|++||.|++|++.. .+|||||+|.+.++|++|+..|||..|.|++|+|+|++++.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~-~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            46899999999999999999999999999999864 48999999999999999999999999999999999998754

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.1e-15  Score=130.05  Aligned_cols=80  Identities=19%  Similarity=0.442  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +.+.++|||+|||.++|+++|+++|++||+|..|++   ....+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            345789999999999999999999999999999874   33468999999999999999999999999999999999997


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=7.5e-15  Score=129.65  Aligned_cols=77  Identities=31%  Similarity=0.508  Sum_probs=71.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe--cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~--~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||+++|+++|+++|++||.|..+++  ....++||||+|.+.++|++||+.|||..|.|++|+|+|+++.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            4458999999999999999999999999999876  3456899999999999999999999999999999999999875

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.3e-15  Score=133.82  Aligned_cols=79  Identities=16%  Similarity=0.387  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +.++|||+|||+++++++|+++|+.||.|.++++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|+++.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            5678999999999999999999999999988763     56789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003463          226 PKDN  229 (818)
Q Consensus       226 pk~~  229 (818)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8764

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.55  E-value=4.5e-15  Score=140.03  Aligned_cols=79  Identities=29%  Similarity=0.471  Sum_probs=72.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      .++|||+|||.++|+++|+++|++||.|++|++     ++.++|||||+|.+.++|.+||+.|||..|.|++|+|+++++
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            357999999999999999999999999999875     456789999999999999999999999999999999999987


Q ss_pred             Cccc
Q 003463          312 GGAR  315 (818)
Q Consensus       312 ~~~r  315 (818)
                      +..+
T Consensus       122 ~~~~  125 (139)
T d1u6fa1         122 GHQR  125 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.55  E-value=6.3e-15  Score=139.02  Aligned_cols=80  Identities=24%  Similarity=0.463  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999874     5778999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76654

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.2e-15  Score=130.57  Aligned_cols=79  Identities=23%  Similarity=0.476  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||+++++++|+++|++||.|..+.     ..++++|||||+|.+.++|++|++.|++..|.|++|+|.++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            467899999999999999999999999999886     257789999999999999999999999999999999999997


Q ss_pred             CCCC
Q 003463          226 PKDN  229 (818)
Q Consensus       226 pk~~  229 (818)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.55  E-value=2.2e-15  Score=133.46  Aligned_cols=81  Identities=22%  Similarity=0.385  Sum_probs=76.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+.++|||+|||.++|+++|+++|++||.|..++..++++|||||+|.+.++|++|++.|++..|.|++|+|.|+.++.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            34578999999999999999999999999999998889999999999999999999999999999999999999998876


Q ss_pred             C
Q 003463          229 N  229 (818)
Q Consensus       229 ~  229 (818)
                      .
T Consensus        93 ~   93 (96)
T d1fjca_          93 G   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.55  E-value=2.1e-15  Score=129.07  Aligned_cols=74  Identities=19%  Similarity=0.229  Sum_probs=66.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      +||||+|||+++|+++|+++|++||.|..+.     ..++++|||||+|.+.++|++|++.|+|..+.|++|.|+++.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999997665     2578899999999999999999999999999999999999986

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.4e-15  Score=130.32  Aligned_cols=77  Identities=27%  Similarity=0.364  Sum_probs=69.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCC-ccCCceEEEEecCCCccc
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-DIAGKRIKLEPSRPGGAR  315 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~-~i~Gr~L~V~~a~~~~~r  315 (818)
                      .+|||+|||.++|+++|+++|++||.|..+++. .++|||||+|.+.++|.+|++.|||. .+.|++|+|+|+.++.+|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~-~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe-cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            379999999999999999999999998876653 45899999999999999999999996 699999999999987654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.1e-14  Score=128.24  Aligned_cols=80  Identities=23%  Similarity=0.405  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ....++|||+|||+++++++|+++|++||+|..|++   ...++|||||+|.+.++|++|++.|++..+.|++|+|.++.
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            345678999999999999999999999999999874   34478999999999999999999999999999999999998


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            764

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.7e-15  Score=127.81  Aligned_cols=74  Identities=30%  Similarity=0.425  Sum_probs=67.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC--ceEEEEe
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G--r~L~V~~  308 (818)
                      ...+|||+|||+.+|+++|+++|++||+|+++++     ++.++|||||+|.+.++|++|++.|||..+.|  ++|+|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            4568999999999999999999999999999875     35678899999999999999999999999998  6699998


Q ss_pred             c
Q 003463          309 S  309 (818)
Q Consensus       309 a  309 (818)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.4e-15  Score=127.56  Aligned_cols=77  Identities=26%  Similarity=0.264  Sum_probs=71.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      .++|||+|||+++|+++|+++|++||.|..+++ ...+|||||+|.+.++|.+|+..|||..|.|+.|+|+|++|+..
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            468999999999999999999999999887776 45789999999999999999999999999999999999998753

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.7e-15  Score=130.95  Aligned_cols=75  Identities=21%  Similarity=0.363  Sum_probs=68.7

Q ss_pred             CccceeeecCC-CCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          236 NQGTLVVFNLD-PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp-~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ...+|||+||| ..+++++|+++|++||.|++|++   ++|||||+|.+.++|.+|++.|||+.|.|++|+|++++++.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            44679999997 56788999999999999999998   47999999999999999999999999999999999998654

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=2.6e-15  Score=129.14  Aligned_cols=75  Identities=23%  Similarity=0.401  Sum_probs=68.2

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCeEEE-Ee-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          240 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-RE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       240 L~V~NLp~~vteedL~~lFs~fG~I~~v-r~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      |||+|||+++|+++|+++|++||.|.++ ++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998654 32     45678999999999999999999999999999999999998876


Q ss_pred             c
Q 003463          314 A  314 (818)
Q Consensus       314 ~  314 (818)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.54  E-value=6.5e-15  Score=127.32  Aligned_cols=75  Identities=24%  Similarity=0.434  Sum_probs=68.2

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCC--ceEEEE
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLE  307 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G--r~L~V~  307 (818)
                      ...++|||+|||.++++++|+++|++||.|.++++     ++.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            34567999999999999999999999999999975     45678999999999999999999999999987  889999


Q ss_pred             ec
Q 003463          308 PS  309 (818)
Q Consensus       308 ~a  309 (818)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4.7e-15  Score=128.38  Aligned_cols=76  Identities=18%  Similarity=0.413  Sum_probs=71.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      .+|||+|||.++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999873     5788999999999999999999999999999999999999765


Q ss_pred             C
Q 003463          228 D  228 (818)
Q Consensus       228 ~  228 (818)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.9e-15  Score=127.92  Aligned_cols=77  Identities=29%  Similarity=0.432  Sum_probs=70.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eCCCcccEEEEEEccHHHHHHHHHHhcCccc-ccccccccccCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPL-RRRKLDIHFSIP  226 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l-~gr~L~V~~a~p  226 (818)
                      .|+++|||+|||.++++++|+++|++||.|..+. ...+.+|||||+|.+.++|.+|+..|+|..+ .|++|+|.|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            3689999999999999999999999999987765 5677899999999999999999999999988 589999999875

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4.8e-15  Score=128.39  Aligned_cols=78  Identities=21%  Similarity=0.328  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      ..++|||+|||+++++++|+++|++||.|..+.+ .+++|||||+|.+.++|++|+..|++..|.|+.|+|+|+.|+..
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            3589999999999999999999999999877764 56899999999999999999999999999999999999988764

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=5.3e-15  Score=127.72  Aligned_cols=74  Identities=24%  Similarity=0.397  Sum_probs=67.1

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCeEEEEec-----C---CCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----P---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       240 L~V~NLp~~vteedL~~lFs~fG~I~~vr~~-----g---~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      |||+|||.++|+++|+++|++||.|+++++.     +   .++|||||+|.+.++|.+|++.|||..+.|++|+|+++++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999998652     1   2478999999999999999999999999999999999875


Q ss_pred             Cc
Q 003463          312 GG  313 (818)
Q Consensus       312 ~~  313 (818)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=6.1e-15  Score=127.33  Aligned_cols=74  Identities=24%  Similarity=0.459  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----C---CCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          155 LFVRNINSNVEDSELRALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       155 LfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~---~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      |||+|||.++|+++|+++|++||.|.++++     +   ++++|||||+|.+.++|++|++.|++..+.|++|.|+++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            899999999999999999999999999873     1   24689999999999999999999999999999999999875


Q ss_pred             CC
Q 003463          227 KD  228 (818)
Q Consensus       227 k~  228 (818)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1.1e-14  Score=126.60  Aligned_cols=77  Identities=29%  Similarity=0.371  Sum_probs=69.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-ecCCCCceEEEEEcCHHHHHHHHHHcCCCcc-CCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-AGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i-~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||.++|+++|+++|++||.|..++ ..++.+++|||+|.+.++|.+|+..|+|..+ .|+.|+|+|+++.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            356899999999999999999999999998764 4667789999999999999999999999988 5899999999863

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=1.1e-14  Score=128.67  Aligned_cols=82  Identities=21%  Similarity=0.464  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhc------Cccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ------NKPLRR  216 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Ln------g~~l~g  216 (818)
                      .....++|||+|||+++|+++|+++|++||+|..+.+     .++++|||||+|.+.++|++|++.|+      |..+.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            3445789999999999999999999999999998873     45689999999999999999999886      567889


Q ss_pred             ccccccccCCCCC
Q 003463          217 RKLDIHFSIPKDN  229 (818)
Q Consensus       217 r~L~V~~a~pk~~  229 (818)
                      ++|+|.++.++..
T Consensus        84 r~l~v~~a~~k~~   96 (98)
T d1x4ha1          84 RQLKVDLAVTRDE   96 (98)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCCc
Confidence            9999999987653

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.1e-15  Score=135.32  Aligned_cols=80  Identities=24%  Similarity=0.451  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      +.+.++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~   84 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999873     577899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003463          224 SIPKD  228 (818)
Q Consensus       224 a~pk~  228 (818)
                      +.++.
T Consensus        85 a~~~~   89 (104)
T d1p1ta_          85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCCC
Confidence            87643

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=6.5e-15  Score=127.81  Aligned_cols=76  Identities=25%  Similarity=0.425  Sum_probs=71.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+|||.++++++|+++|++||+|.+|++. +.++||||+|.+.++|.+|++.|||..|.|++|+|+||.++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~-~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            4579999999999999999999999999999985 457999999999999999999999999999999999998764

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=6.1e-15  Score=126.09  Aligned_cols=72  Identities=17%  Similarity=0.367  Sum_probs=68.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            6999999999999999999999999999984     47789999999999999999999999999999999999984

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.53  E-value=6.5e-15  Score=127.73  Aligned_cols=76  Identities=22%  Similarity=0.384  Sum_probs=67.0

Q ss_pred             CccceeeecCCCCCC-HHHHHHHhhccCCeEEEEe------cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          236 NQGTLVVFNLDPSVS-NEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       236 ~~~tL~V~NLp~~vt-eedL~~lFs~fG~I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      ..++|||+|||.++| +++|+++|++||.|.+|++      ++.++|||||+|.+.++|++|++ |||..+.|++|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            356899999999986 4569999999999999975      34568899999999999999995 999999999999999


Q ss_pred             cCCC
Q 003463          309 SRPG  312 (818)
Q Consensus       309 a~~~  312 (818)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1.2e-14  Score=128.34  Aligned_cols=78  Identities=18%  Similarity=0.349  Sum_probs=72.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      .++++|||+|||+++|+++|+++|++||.|..+.+  ....+|||||+|.+.++|++|++.|++..|.|++|+|+|+++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            45679999999999999999999999999999884  4567899999999999999999999999999999999998754

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.53  E-value=9.4e-15  Score=126.28  Aligned_cols=74  Identities=24%  Similarity=0.458  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccc--ccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHF  223 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~  223 (818)
                      ..++|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|++..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            4678999999999999999999999999999873     57789999999999999999999999999976  8899988


Q ss_pred             c
Q 003463          224 S  224 (818)
Q Consensus       224 a  224 (818)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=4.4e-15  Score=133.20  Aligned_cols=78  Identities=23%  Similarity=0.391  Sum_probs=71.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      .++|||+|||.++|+++|+++|++||+|.+|++     ++.++|||||+|.+.++|.+|++.|||..|.|++|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999875     456689999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003463          312 GGA  314 (818)
Q Consensus       312 ~~~  314 (818)
                      +..
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            653

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=8.4e-15  Score=132.46  Aligned_cols=76  Identities=17%  Similarity=0.267  Sum_probs=70.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||+++++++|+++|++||+|..|++. ..++||||+|.+.++|.+|++.|||..|.|++|+|+|+...
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            34689999999999999999999999999999984 57899999999999999999999999999999999998654

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1.2e-14  Score=130.31  Aligned_cols=80  Identities=26%  Similarity=0.343  Sum_probs=71.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEe
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  308 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~  308 (818)
                      +...++|||+|||+.+|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+.+++ .|.|++|+|++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            344567999999999999999999999999999975     466799999999999999999998876 79999999999


Q ss_pred             cCCCcc
Q 003463          309 SRPGGA  314 (818)
Q Consensus       309 a~~~~~  314 (818)
                      +..+..
T Consensus        86 a~~~~~   91 (103)
T d2cqda1          86 AYLGAK   91 (103)
T ss_dssp             STTTCC
T ss_pred             cCCCCC
Confidence            976543

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=5.3e-15  Score=129.04  Aligned_cols=77  Identities=17%  Similarity=0.361  Sum_probs=71.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ..+|||+|||+++++++|+++|++||.|..+++   ...++|||||+|.+.++|++|++.|+|..|.|++|.|.++.++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            468999999999999999999999999999884   34578999999999999999999999999999999999998765

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.3e-15  Score=133.77  Aligned_cols=77  Identities=21%  Similarity=0.440  Sum_probs=70.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++     ++.++|||||+|.+.++|.+|+. |||..|.|+.|+|.+++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            4468999999999999999999999999999975     46789999999999999999995 99999999999999986


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      ++.
T Consensus        96 ~~~   98 (101)
T d2cq4a1          96 AEK   98 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=6.9e-15  Score=125.52  Aligned_cols=74  Identities=22%  Similarity=0.424  Sum_probs=68.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      .++|||+|++  +|+++|+++|++||.|.+|++. +.++||||+|.+.++|.+|+++|||..+.|++|+|+|++++.
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~-~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeec-cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            4689999996  8999999999999999999985 467899999999999999999999999999999999998754

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=6.9e-15  Score=126.48  Aligned_cols=72  Identities=22%  Similarity=0.444  Sum_probs=67.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      .++++|||+|||.++|+++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            46789999999999999999999999999999873     4778999999999999999999999999999999886

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=7.6e-15  Score=124.93  Aligned_cols=72  Identities=22%  Similarity=0.443  Sum_probs=68.1

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      +|||+|||+++++++|+++|++||.|..+++    +++++|||||+|.+.++|++|++.|+|..+.|++|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999999999999999999999999984    56789999999999999999999999999999999999874

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=6.6e-15  Score=133.17  Aligned_cols=77  Identities=13%  Similarity=0.268  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      +.+++|||+|||+++++++|+++|++||+|..|.+ .+.+|||||+|.+.++|++|++.|+|..|.|++|.|.|+...
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            35689999999999999999999999999999986 567899999999999999999999999999999999998543

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.5e-14  Score=130.37  Aligned_cols=77  Identities=25%  Similarity=0.380  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          152 SRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       152 srtLfV~NLP~-~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      +++|||+|||+ .+|+++|+++|++||+|..|++....+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+....
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            58999999965 599999999999999999999877779999999999999999999999999999999999986543

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.2e-14  Score=129.74  Aligned_cols=77  Identities=12%  Similarity=0.242  Sum_probs=70.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ...++|||+|||.++++++|+++|++||+|..+.+    +++++|||||+|.+.++|++|++.|||..|.|+++.|.++.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            45689999999999999999999999999988762    56789999999999999999999999999999999998776


Q ss_pred             C
Q 003463          226 P  226 (818)
Q Consensus       226 p  226 (818)
                      |
T Consensus        96 P   96 (101)
T d1x5oa1          96 P   96 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=3.6e-15  Score=129.95  Aligned_cols=79  Identities=24%  Similarity=0.459  Sum_probs=73.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~~  229 (818)
                      ..+++|||+|||.++||++|+++|++||+|.+|++...++|||||+|.+.++|++|+.  ++..|.|++|.|.++.++..
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            4679999999999999999999999999999999888899999999999999999996  78889999999999987764


Q ss_pred             C
Q 003463          230 P  230 (818)
Q Consensus       230 ~  230 (818)
                      .
T Consensus        81 ~   81 (88)
T d1wf0a_          81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.3e-14  Score=124.84  Aligned_cols=71  Identities=28%  Similarity=0.518  Sum_probs=65.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEE
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  306 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V  306 (818)
                      ..++|||+|||+.+|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            3568999999999999999999999999999875     3566889999999999999999999999999999987

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.3e-14  Score=127.04  Aligned_cols=78  Identities=14%  Similarity=0.324  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+++|||+|||+++|+++|+++|++||.|..|++     +++++|||||+|.+.++|++||+.  ...|.|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            45789999999999999999999999999999873     588999999999999999999985  44789999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87653

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=5e-15  Score=129.04  Aligned_cols=77  Identities=19%  Similarity=0.333  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ..++|||+|||+++|+++|+++|++||.|.+|++...+++||||+|.+.++|++|+.  ++..|.|++|+|++++++..
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            356899999999999999999999999999999988889999999999999999996  88899999999999987654

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.5e-14  Score=125.10  Aligned_cols=73  Identities=25%  Similarity=0.409  Sum_probs=66.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccc--cccccccc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFS  224 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~a  224 (818)
                      .++|||+|||.++|+++|+++|++||+|.++++     +++++|||||+|.+.++|++|++.|+|..+.|  ++|+|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            578999999999999999999999999999873     46789999999999999999999999999987  45888775

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.9e-14  Score=129.00  Aligned_cols=79  Identities=25%  Similarity=0.419  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++ .|.|++|.|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            4578999999999999999999999999999984     467899999999999999999998775 7999999999987


Q ss_pred             CCCCC
Q 003463          226 PKDNP  230 (818)
Q Consensus       226 pk~~~  230 (818)
                      .+..+
T Consensus        88 ~~~~p   92 (103)
T d2cqda1          88 LGAKP   92 (103)
T ss_dssp             TTCCC
T ss_pred             CCCCC
Confidence            65543

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.1e-14  Score=129.62  Aligned_cols=80  Identities=25%  Similarity=0.360  Sum_probs=70.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEE--------E-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--------R-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  301 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v--------r-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G  301 (818)
                      ....+|||+|||..+|+++|+++|+.||.|..+        .     .++..++||||+|.+.++|.+|++.|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            456799999999999999999999999988643        1     135678999999999999999999999999999


Q ss_pred             ceEEEEecCCCcc
Q 003463          302 KRIKLEPSRPGGA  314 (818)
Q Consensus       302 r~L~V~~a~~~~~  314 (818)
                      ++|+|++++++..
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987653

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.6e-14  Score=127.97  Aligned_cols=76  Identities=14%  Similarity=0.326  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      +.++|||+|||.++++++|+++|++||+|.+|++. +.+|||||+|.+.++|++|+..|+|..|.|+.|+|.|++++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~-~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEE-ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            45799999999999999999999999999999864 46999999999999999999999999999999999998764

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.1e-14  Score=130.74  Aligned_cols=77  Identities=17%  Similarity=0.306  Sum_probs=70.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      .++|||+|||+++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++ ++|..|.|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            368999999999999999999999999999976     35678999999999999999996 899999999999999998


Q ss_pred             Ccc
Q 003463          312 GGA  314 (818)
Q Consensus       312 ~~~  314 (818)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=8.4e-15  Score=130.65  Aligned_cols=80  Identities=29%  Similarity=0.346  Sum_probs=72.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEE-----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr-----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||.++++++|+++|++||.|..++     .++..++||||+|.+.++|.+|++.|||..|.|++|+|+|++
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            356899999999999999999999999887763     357789999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003463          311 PGGAR  315 (818)
Q Consensus       311 ~~~~r  315 (818)
                      ++.++
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            87654

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1e-14  Score=127.70  Aligned_cols=79  Identities=23%  Similarity=0.593  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHH----HhhcCCCEEEEEe--CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRA----LFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~----lFs~fG~I~~v~~--~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      +|+++|||+|||.+++++||++    +|++||+|..|++  +++++|||||+|.+.++|++|++.+++..+.|+.|.|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4789999999999999999864    6899999999985  356799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003463          224 SIPKD  228 (818)
Q Consensus       224 a~pk~  228 (818)
                      +.++.
T Consensus        81 ak~~~   85 (91)
T d1nu4a_          81 AKTDS   85 (91)
T ss_dssp             CSSCC
T ss_pred             eCCCc
Confidence            98654

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=3.7e-14  Score=125.27  Aligned_cols=77  Identities=22%  Similarity=0.396  Sum_probs=69.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcC------CCccCCceEE
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN------RSDIAGKRIK  305 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~Ln------G~~i~Gr~L~  305 (818)
                      .++|||+|||+++|+++|+++|++||.|.++++     .+.++|||||+|.+.++|.+|++.|+      |..+.|++|+
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~   87 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLK   87 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEE
Confidence            468999999999999999999999999998865     44578999999999999999999987      5678999999


Q ss_pred             EEecCCCc
Q 003463          306 LEPSRPGG  313 (818)
Q Consensus       306 V~~a~~~~  313 (818)
                      |++++++.
T Consensus        88 v~~a~~k~   95 (98)
T d1x4ha1          88 VDLAVTRD   95 (98)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99998865

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=1.9e-14  Score=124.78  Aligned_cols=76  Identities=32%  Similarity=0.566  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      .++|||+|||.++++++|+++|++||+|.+|++. +.+|||||+|.+.++|++|++.|+|..|.|++|+|+|+.++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~-~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            4689999999999999999999999999999863 568999999999999999999999999999999999997654

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=3e-14  Score=120.42  Aligned_cols=72  Identities=15%  Similarity=0.335  Sum_probs=65.7

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       240 L~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      |||+|||+++++++|+++|++|| +..+++ +.++|+|||+|.+.++|.+|++.|||..+.|++|+|++++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 555555 4678999999999999999999999999999999999997653

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2.6e-14  Score=125.12  Aligned_cols=77  Identities=21%  Similarity=0.391  Sum_probs=69.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+.  +..|.|+.|.|+++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            4568999999999999999999999999999964     567799999999999999999984  458999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8654

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=4.7e-15  Score=126.94  Aligned_cols=76  Identities=22%  Similarity=0.367  Sum_probs=68.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCc-ccccccccccccCCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK-PLRRRKLDIHFSIPKDN  229 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~-~l~gr~L~V~~a~pk~~  229 (818)
                      .+|||+|||.++|+++|+++|++||.|..+++ .+.+|||||+|.+.++|++|++.|+|. .+.|++|+|.++.|+..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE-EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEE-ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            47999999999999999999999999876543 357899999999999999999999996 59999999999998764

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.2e-14  Score=126.74  Aligned_cols=75  Identities=13%  Similarity=0.290  Sum_probs=66.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+|||++++++||+++|++|| ++.+++ +..++||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            45899999999999999999999999 333333 4568999999999999999999999999999999999997653

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=7.3e-15  Score=126.26  Aligned_cols=75  Identities=20%  Similarity=0.481  Sum_probs=68.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEE-E-----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          155 LFVRNINSNVEDSELRALFEQYGDIRTL-Y-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       155 LfV~NLP~~vTEeeLr~lFs~fG~I~~v-~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      |||+|||.++|+++|+++|++||.|..+ +     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998553 3     246789999999999999999999999999999999999998765


Q ss_pred             C
Q 003463          229 N  229 (818)
Q Consensus       229 ~  229 (818)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=6e-15  Score=131.62  Aligned_cols=80  Identities=21%  Similarity=0.406  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .|+++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4789999999999999999999999999876654     36889999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .+++.
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            88664

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.6e-14  Score=128.53  Aligned_cols=81  Identities=22%  Similarity=0.372  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-------------eCCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------------TACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-------------~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                      .....++|||+|||.++|+++|+++|+.||.|..+.             .+++++|||||+|.+.++|++|++.|+|..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            445678999999999999999999999999885432             1467889999999999999999999999999


Q ss_pred             ccccccccccCCCC
Q 003463          215 RRRKLDIHFSIPKD  228 (818)
Q Consensus       215 ~gr~L~V~~a~pk~  228 (818)
                      .|++|+|.++.++.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998754

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.49  E-value=1.2e-14  Score=125.98  Aligned_cols=76  Identities=18%  Similarity=0.394  Sum_probs=67.5

Q ss_pred             CCcEEEEcCCCCCCc-HHHHHHHhhcCCCEEEEEe------CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccc
Q 003463          151 PSRTLFVRNINSNVE-DSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  223 (818)
Q Consensus       151 ~srtLfV~NLP~~vT-EeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~  223 (818)
                      ..++|||+|||.+++ +++|+++|++||+|..|++      +++++|||||+|.+.++|++|++ |++..+.|+.|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999986 5569999999999999973      45689999999999999999996 999999999999999


Q ss_pred             cCCC
Q 003463          224 SIPK  227 (818)
Q Consensus       224 a~pk  227 (818)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=1.9e-14  Score=128.56  Aligned_cols=77  Identities=21%  Similarity=0.278  Sum_probs=69.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ..++|||+|||+++++++|+++|++||.|..+++    ++.++|||||+|.+.++|.+|++.|||..|.|+++.|.+++|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            3468999999999999999999999999988864    455688999999999999999999999999999999988876


Q ss_pred             C
Q 003463          312 G  312 (818)
Q Consensus       312 ~  312 (818)
                      -
T Consensus        97 l   97 (101)
T d1x5oa1          97 L   97 (101)
T ss_dssp             B
T ss_pred             c
Confidence            3

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=5.9e-14  Score=124.33  Aligned_cols=77  Identities=22%  Similarity=0.409  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCC--ceEEEEecCCCc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  313 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~G--r~L~V~~a~~~~  313 (818)
                      ..++|||+|||+++++++|+++|++||.|+.+++. ..+++|||+|.+.++|++|++.||+..|.|  ++|+|+|++++.
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee-ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            45799999999999999999999999999999985 457899999999999999999999999987  589999998754

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.1e-14  Score=128.57  Aligned_cols=81  Identities=21%  Similarity=0.286  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEEccHHHHHHHHHHhcCccc--ccccccccccC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l--~gr~L~V~~a~  225 (818)
                      ..+..+|||+|||+++|+++|+++|++||.|..|.+ ..+.+|||||+|.+.++|++|++.|++..|  .+++|+|.|+.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            356789999999999999999999999999999874 345789999999999999999999999998  57889999987


Q ss_pred             CCCC
Q 003463          226 PKDN  229 (818)
Q Consensus       226 pk~~  229 (818)
                      ++..
T Consensus        84 ~~~~   87 (108)
T d2adba1          84 LTSL   87 (108)
T ss_dssp             SCSC
T ss_pred             Cccc
Confidence            7654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=1.3e-14  Score=126.09  Aligned_cols=73  Identities=21%  Similarity=0.187  Sum_probs=67.8

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCc
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  313 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~  313 (818)
                      +|||+|||+++|+++|+++|++||.|.++++.  .+|||||+|.+.++|++||+.|||..|.|+.|+|.+++++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            69999999999999999999999999999984  35899999999999999999999999999999999876543

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.7e-14  Score=122.44  Aligned_cols=74  Identities=23%  Similarity=0.447  Sum_probs=68.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||.++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3579999999999999999999999999999873     57899999999999999999998 69999999999998764

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.1e-14  Score=126.58  Aligned_cols=76  Identities=28%  Similarity=0.520  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCC-CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          150 HPSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       150 ~~srtLfV~NLP-~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ...++|||+||| ..+++++|+++|++||.|..|++   ++|||||+|.+.++|++|++.|+|..|.|++|+|.++.++.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            345789999997 57889999999999999999987   68999999999999999999999999999999999997643

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.9e-14  Score=125.16  Aligned_cols=82  Identities=21%  Similarity=0.336  Sum_probs=71.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEe------CCCcccEEEEEEccHHHHHHHHHHhcC--ccccccccccc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGD-IRTLYT------ACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIH  222 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~-I~~v~~------~~ksrG~AFV~F~d~e~A~~Al~~Lng--~~l~gr~L~V~  222 (818)
                      +++|||+|||.++++++|+++|++||+ |..+.+      .++++|||||+|.+.++|.+|++.|++  ..+.|++|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 888874      367899999999999999999999865  45579999999


Q ss_pred             ccCCCCCCCCC
Q 003463          223 FSIPKDNPSDK  233 (818)
Q Consensus       223 ~a~pk~~~~~~  233 (818)
                      |+.|+..+..+
T Consensus        81 ~A~p~~~~~~~   91 (96)
T d2disa1          81 WAEPEIDVDED   91 (96)
T ss_dssp             ESCSSCSTTTC
T ss_pred             EcCCCCCCChH
Confidence            99987766443

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=2.5e-14  Score=125.22  Aligned_cols=78  Identities=22%  Similarity=0.448  Sum_probs=70.2

Q ss_pred             ccceeeecCCCCCCHHHHHH----HhhccCCeEEEEec--CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~----lFs~fG~I~~vr~~--g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      .++|||+|||+.++++||++    +|++||+|.+|++.  +..+|||||+|.+.++|.+|++.|||..+.|+.|+|.||+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak   82 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   82 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            46899999999999999864    68999999999863  3468999999999999999999999999999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      ++..
T Consensus        83 ~~~~   86 (91)
T d1nu4a_          83 TDSD   86 (91)
T ss_dssp             SCCT
T ss_pred             CCch
Confidence            8654

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=4.1e-14  Score=119.45  Aligned_cols=70  Identities=20%  Similarity=0.371  Sum_probs=64.3

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +|||+|||+++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++ +++..|.|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            4899999999999999999999999999975     46678999999999999999997 7999999999999654

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.47  E-value=9.1e-15  Score=128.26  Aligned_cols=76  Identities=24%  Similarity=0.335  Sum_probs=69.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...+|||+|||+++|+++|+++|+.||.|..+++    +++++|||||+|.+.++|.+|++ |||..+.|++|+|++++.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            4568999999999999999999999998877643    67789999999999999999996 999999999999999986


Q ss_pred             C
Q 003463          312 G  312 (818)
Q Consensus       312 ~  312 (818)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=6.7e-14  Score=121.62  Aligned_cols=80  Identities=24%  Similarity=0.342  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHh--cCcccccccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~L--ng~~l~gr~L~V~~a~  225 (818)
                      ...|+++|||+|||.++++++|+++|++||.|..+++ .+.++||||+|.+.++|++|++.+  ++..+.|++|+|.|+.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~-~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccc-cccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            3468999999999999999999999999999999975 356899999999999999999866  4678999999999997


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=2.8e-14  Score=121.65  Aligned_cols=75  Identities=20%  Similarity=0.366  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      ...++|||+||+  +|+++|+++|++||+|.++++ .+.+|||||+|.+.++|++|++.|+|..+.|++|+|.|++++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            456899999995  899999999999999999986 457899999999999999999999999999999999999764

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=5.6e-14  Score=121.27  Aligned_cols=73  Identities=19%  Similarity=0.340  Sum_probs=67.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      .++|||+|||.++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++ +++..|.|++|+|+.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            468999999999999999999999999999875     46779999999999999999997 69999999999998874

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=2.8e-14  Score=124.29  Aligned_cols=76  Identities=14%  Similarity=0.309  Sum_probs=67.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      .+++|||+|||++++++||+++|++||. ..+. ..+.+|||||+|.+.++|++|++.|++..|.|++|+|+++..+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~-~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCY-VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEE-EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeee-eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4689999999999999999999999992 2232 25689999999999999999999999999999999999986544

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=2.6e-14  Score=128.31  Aligned_cols=77  Identities=18%  Similarity=0.436  Sum_probs=71.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      .++|||+|||+++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++ +++..|.|+.|.|.++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            479999999999999999999999999999884     46789999999999999999997 799999999999999988


Q ss_pred             CCC
Q 003463          227 KDN  229 (818)
Q Consensus       227 k~~  229 (818)
                      ++.
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.2e-14  Score=119.37  Aligned_cols=70  Identities=14%  Similarity=0.386  Sum_probs=64.7

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +|||+|||+++||++|+++|++||+|..+.+     +++++|||||+|.+.++|++|++ +++..|.|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            4899999999999999999999999999983     57889999999999999999998 7999999999998753

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=3.9e-14  Score=119.02  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=64.7

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +|||+|||+++|+++|+++|++||.|..+.+     ++..+++|||+|.+.++|.+|++ |||+.|.|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            4899999999999999999999999999864     45678999999999999999996 9999999999999875

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=4.1e-14  Score=120.23  Aligned_cols=72  Identities=24%  Similarity=0.484  Sum_probs=66.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      .++|||+|||+++|+++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++ +++..|.|++|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            479999999999999999999999999999873     66789999999999999999997 8999999999999865

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=7.3e-14  Score=123.72  Aligned_cols=77  Identities=29%  Similarity=0.515  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccc--ccccccccCCC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPK  227 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~g--r~L~V~~a~pk  227 (818)
                      .|+++|||+|||+++++++|+++|++||+|..+++. +.++||||+|.+.++|++|++.|++..|.|  ++|+|.|+++.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee-ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            478999999999999999999999999999999864 468999999999999999999999999986  57999998754

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=2.4e-14  Score=121.69  Aligned_cols=71  Identities=28%  Similarity=0.443  Sum_probs=65.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      .+|||+|||+++|+++|+++|++||.|+++++     ++.++|||||+|.+.++|.+|++ ++++.++|+.|+|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            36999999999999999999999999998864     46789999999999999999997 7999999999999876

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=8.5e-14  Score=124.59  Aligned_cols=80  Identities=16%  Similarity=0.382  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      ..|.++|||+|||+++|+++|+++|++|| |..+++      .++++|||||+|.+.++|++|++ |++..|.|++|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            45679999999999999999999999999 666552      46788999999999999987775 99999999999999


Q ss_pred             ccCCCCCC
Q 003463          223 FSIPKDNP  230 (818)
Q Consensus       223 ~a~pk~~~  230 (818)
                      ++.++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=7.8e-14  Score=123.93  Aligned_cols=79  Identities=14%  Similarity=0.217  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          149 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       149 e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      ....++|||+|||+++++++|+++|++||+|..+.+.  .+|||||+|.+.++|++||+.||+..|.|+.|+|.+..++.
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            3456789999999999999999999999999999863  57999999999999999999999999999999999987654


Q ss_pred             C
Q 003463          229 N  229 (818)
Q Consensus       229 ~  229 (818)
                      .
T Consensus        90 ~   90 (98)
T d1wg4a_          90 E   90 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=2.6e-14  Score=129.13  Aligned_cols=77  Identities=25%  Similarity=0.305  Sum_probs=69.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCeEEEEec-CCCCceEEEEEcCHHHHHHHHHHcCCCcc--CCceEEEEecCCCc
Q 003463          237 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDI--AGKRIKLEPSRPGG  313 (818)
Q Consensus       237 ~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~-g~srG~aFVeF~d~e~A~~Ai~~LnG~~i--~Gr~L~V~~a~~~~  313 (818)
                      ..+|||+|||+.+|+++|+++|++||.|.+|++. .+++|+|||+|.+.++|++|++.|||..|  .|++|+|.|++++.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            4579999999999999999999999999998763 34678999999999999999999999988  47899999998765

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=7.3e-14  Score=118.69  Aligned_cols=71  Identities=18%  Similarity=0.359  Sum_probs=65.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ++|||+|||+++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++ ++|+.|.|+.|+|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            58999999999999999999999999999865     45678999999999999999985 8999999999999876

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=2.2e-14  Score=128.34  Aligned_cols=75  Identities=17%  Similarity=0.385  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++|||+|||.++++++|+++|+.||+|.+|++     +++++|||||+|.+.++|++|++ |+|..|.|+.|.|+++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            4579999999999999999999999999999984     57899999999999999999996 99999999999999875


Q ss_pred             C
Q 003463          226 P  226 (818)
Q Consensus       226 p  226 (818)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=1.9e-14  Score=122.35  Aligned_cols=71  Identities=17%  Similarity=0.428  Sum_probs=65.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ++|||+|||+++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..+.|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            57999999999999999999999999988773     57899999999999999999998 7999999999999875

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=4.2e-14  Score=122.75  Aligned_cols=74  Identities=15%  Similarity=0.181  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  228 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk~  228 (818)
                      .+|||+|||+++++++|+++|++||+|..+++.  .+|||||+|.+.++|++||+.|+|..|.|+.|+|.++.++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            369999999999999999999999999999864  35999999999999999999999999999999999876543

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=2.4e-13  Score=121.87  Aligned_cols=82  Identities=15%  Similarity=0.228  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhc--CcccccccccccccC
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLDIHFSI  225 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Ln--g~~l~gr~L~V~~a~  225 (818)
                      ...++++|||+|||.++||++|+++|++||.|..+++ .+.+|+|||+|.+.++|++|++.++  +..+.|++|+|.|+.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~-~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~   89 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEE-EecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcC
Confidence            3457899999999999999999999999999999986 4578999999999999999999874  566889999999997


Q ss_pred             CCCCC
Q 003463          226 PKDNP  230 (818)
Q Consensus       226 pk~~~  230 (818)
                      .+...
T Consensus        90 ~~~~~   94 (104)
T d1wexa_          90 SKRIT   94 (104)
T ss_dssp             SSSCC
T ss_pred             CCccC
Confidence            65543

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=6.2e-14  Score=124.57  Aligned_cols=77  Identities=21%  Similarity=0.184  Sum_probs=70.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      ...+|||+|||+.++++||+++|++||+|+.+++.  ++|||||+|.+.++|++||+.|||..|.|+.|+|.+++....
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            34589999999999999999999999999999885  468999999999999999999999999999999999876543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.6e-13  Score=119.15  Aligned_cols=79  Identities=15%  Similarity=0.178  Sum_probs=70.7

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc--CCCccCCceEEEEecCC
Q 003463          234 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       234 ~~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~  311 (818)
                      ....++|||+|||.++++++|+++|++||.|.++++. ..+++|||+|.+.++|++|++.+  ++..+.|++|+|.|++.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~-~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc-ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3456799999999999999999999999999999885 45789999999999999999865  56789999999999986


Q ss_pred             Cc
Q 003463          312 GG  313 (818)
Q Consensus       312 ~~  313 (818)
                      +.
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.44  E-value=1.3e-14  Score=127.30  Aligned_cols=77  Identities=16%  Similarity=0.216  Sum_probs=69.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      ...++|||+|||.++|+++|+++|++||.|..++    .+++++|||||+|.+.++|++||+ |++..+.|++|+|.++.
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            3467999999999999999999999999876654    367899999999999999999996 99999999999999987


Q ss_pred             CC
Q 003463          226 PK  227 (818)
Q Consensus       226 pk  227 (818)
                      .+
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=9.8e-14  Score=117.18  Aligned_cols=71  Identities=18%  Similarity=0.450  Sum_probs=64.9

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccccccCCC
Q 003463          155 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  227 (818)
Q Consensus       155 LfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~pk  227 (818)
                      |||+|||+++++++|+++|++|| +..+++ .+.+|||||+|.+.++|++|++.|+|..+.|++|+|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555543 678999999999999999999999999999999999998643

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.1e-13  Score=122.11  Aligned_cols=78  Identities=19%  Similarity=0.229  Sum_probs=68.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCC-eEEEEe------cCCCCceEEEEEcCHHHHHHHHHHcCCC--ccCCceEEEEe
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEP  308 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~-I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~LnG~--~i~Gr~L~V~~  308 (818)
                      ++|||+|||.++|+++|+++|++||. |..+++      .+.++|||||+|.+.++|.+|++.|++.  .+.|+.|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            47999999999999999999999996 888876      2457899999999999999999999754  55799999999


Q ss_pred             cCCCccc
Q 003463          309 SRPGGAR  315 (818)
Q Consensus       309 a~~~~~r  315 (818)
                      |+|+...
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9987644

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=6.4e-14  Score=118.42  Aligned_cols=70  Identities=23%  Similarity=0.453  Sum_probs=64.2

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          239 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       239 tL~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      +|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+ +++..+.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            4899999999999999999999999999975     46679999999999999999997 5888999999999865

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=2e-13  Score=122.07  Aligned_cols=77  Identities=23%  Similarity=0.364  Sum_probs=66.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe------cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~------~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...+|||+|||+++|+++|+++|++|| |+++++      ++.++|||||+|.+.++|++|+ .||+..|.|++|+|+++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            346999999999999999999999999 666643      3557899999999999998776 59999999999999999


Q ss_pred             CCCcc
Q 003463          310 RPGGA  314 (818)
Q Consensus       310 ~~~~~  314 (818)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T d1wi8a_          92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=5.9e-14  Score=118.64  Aligned_cols=70  Identities=19%  Similarity=0.469  Sum_probs=64.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ .++..|.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            5999999999999999999999999999983     57899999999999999999998 5778899999988764

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=3.2e-13  Score=121.01  Aligned_cols=78  Identities=18%  Similarity=0.185  Sum_probs=70.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc--CCCccCCceEEEEecCCC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~~  312 (818)
                      ...++|||+|||..+|++||+++|++||.|+.+++. +.+++|||+|++.++|++|+..|  ++..+.|++|+|.|++.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~-~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE-ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            346799999999999999999999999999999985 46799999999999999999988  556788999999999765


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        92 ~   92 (104)
T d1wexa_          92 R   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            4

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=1.2e-13  Score=119.50  Aligned_cols=73  Identities=12%  Similarity=0.348  Sum_probs=67.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..++|||+|||.++|+++|+++|+.||.|..|++    +++++|||||+|.+.++|++|++ +++..+.|+.|.|.+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            3689999999999999999999999999999984    56789999999999999999997 7999999999999875

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=5.9e-14  Score=117.88  Aligned_cols=70  Identities=16%  Similarity=0.401  Sum_probs=64.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          154 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       154 tLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +|||+|||+++||++|+++|++||.|..+.+     +++.+|||||+|.+.++|++|++ +++..|.|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            5999999999999999999999999998873     56789999999999999999997 9999999999999865

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=1.5e-13  Score=118.73  Aligned_cols=74  Identities=9%  Similarity=0.166  Sum_probs=67.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ..++|||+|||.++|+++|+++|+.||.|..|++    ++.++|||||+|.+.++|.+|++ ++|..+.|+.|+|.+++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4568999999999999999999999999999976    34568999999999999999996 79999999999999853

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=9.6e-14  Score=121.09  Aligned_cols=72  Identities=14%  Similarity=0.385  Sum_probs=63.8

Q ss_pred             CccceeeecCCCCCCHHHH---HHHhhccCCeEEEEec-----C---CCCceEEEEEcCHHHHHHHHHHcCCCccCCceE
Q 003463          236 NQGTLVVFNLDPSVSNEDL---RQIFGAYGEVKEIRET-----P---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  304 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL---~~lFs~fG~I~~vr~~-----g---~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L  304 (818)
                      ..++|||+|||++++++||   +++|++||.|..|++.     +   ..+|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3457999999999999999   6789999999999762     1   224799999999999999999999999999999


Q ss_pred             EEE
Q 003463          305 KLE  307 (818)
Q Consensus       305 ~V~  307 (818)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.42  E-value=1.9e-13  Score=115.40  Aligned_cols=71  Identities=20%  Similarity=0.207  Sum_probs=64.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEec---CCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~---g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      .+|||+|||+++++++|+++|+.||.|+.+++.   ...+++|||+|.+.++|.+|+. ++++.|+|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            379999999999999999999999999999762   3446799999999999999985 8999999999999864

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=1e-13  Score=115.71  Aligned_cols=66  Identities=23%  Similarity=0.437  Sum_probs=62.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccc
Q 003463          155 LFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  220 (818)
Q Consensus       155 LfV~NLP~~vTEeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~  220 (818)
                      |||+|||.++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999999873     567899999999999999999999999999999875

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=2.2e-13  Score=121.09  Aligned_cols=78  Identities=19%  Similarity=0.178  Sum_probs=69.3

Q ss_pred             CCccceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHH--HcCCCccCCceEEEEecCC
Q 003463          235 LNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNRSDIAGKRIKLEPSRP  311 (818)
Q Consensus       235 ~~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~--~LnG~~i~Gr~L~V~~a~~  311 (818)
                      ...++|||+|||.+ +|+++|.++|++||.|.++++. ..+++|||+|.+.++|.+|++  .+++..+.|++|+|.||+.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~-~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEe-ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            34568999999985 8999999999999999999985 457999999999999999998  5788899999999999975


Q ss_pred             Cc
Q 003463          312 GG  313 (818)
Q Consensus       312 ~~  313 (818)
                      +.
T Consensus        95 ~~   96 (99)
T d1x4fa1          95 YK   96 (99)
T ss_dssp             CS
T ss_pred             cc
Confidence            43

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=6.9e-14  Score=116.77  Aligned_cols=66  Identities=24%  Similarity=0.439  Sum_probs=61.2

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCeEEEEe-----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          240 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       240 L~V~NLp~~vteedL~~lFs~fG~I~~vr~-----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      |||+|||.++|+++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999999864     456789999999999999999999999999998764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=1.5e-13  Score=118.67  Aligned_cols=74  Identities=22%  Similarity=0.293  Sum_probs=65.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEE-E----EecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-I----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~-v----r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ...+|||+|||++++++||+++|+.||.|.. +    +.++.++|+|||+|.+.++|.+|++.||++.+.|++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3457999999999999999999999998754 2    235677899999999999999999999999999999999875

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=5.7e-13  Score=116.17  Aligned_cols=77  Identities=17%  Similarity=0.233  Sum_probs=68.6

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHc--CCCccCCceEEEEecCCC
Q 003463          236 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~-vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~L--nG~~i~Gr~L~V~~a~~~  312 (818)
                      ..++|||+|||.. +|++||.++|++||.|.+|++. ..+++|||+|++.++|.+|++.|  ++..+.|++|+|.||+..
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~-~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEee-ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            4578999999986 7899999999999999999985 35689999999999999999966  677899999999999754


Q ss_pred             c
Q 003463          313 G  313 (818)
Q Consensus       313 ~  313 (818)
                      .
T Consensus        86 ~   86 (89)
T d1x4da1          86 K   86 (89)
T ss_dssp             T
T ss_pred             c
Confidence            3

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.37  E-value=3.3e-13  Score=113.84  Aligned_cols=71  Identities=17%  Similarity=0.254  Sum_probs=64.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ++|||+|||+++++++|+++|+.||+|..+++   ....++||||+|.+.++|++|++ +++..|.|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999874   34456899999999999999996 8999999999998754

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=9.8e-13  Score=117.73  Aligned_cols=78  Identities=23%  Similarity=0.249  Sum_probs=68.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEE-E----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-R----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v-r----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      .+..+|||+|||+++|++||+++|..||.|..+ .    .++.++|+|||+|.+.++|++|++ +|+..|.||.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            355689999999999999999999999988764 2    255678999999999999999996 9999999999999999


Q ss_pred             CCCc
Q 003463          310 RPGG  313 (818)
Q Consensus       310 ~~~~  313 (818)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            8764

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=9.5e-13  Score=117.84  Aligned_cols=79  Identities=11%  Similarity=0.153  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....+|||+|||+++|+++|+++|..+|.|..+.     .+++.+|||||+|.+.++|++|++ +++..|.||.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            3556899999999999999999999999987754     356789999999999999999997 8999999999999998


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .+++.
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            77653

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=2.6e-13  Score=121.87  Aligned_cols=79  Identities=18%  Similarity=0.218  Sum_probs=69.9

Q ss_pred             CccceeeecCCCCC-CH----HHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSV-SN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~v-te----edL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+||+.++ ++    ++|+++|++||.|+++++. +++++|||+|.+.++|.+|++.|||..|.|++|+|.|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            34689999999886 33    5699999999999999885 568899999999999999999999999999999999998


Q ss_pred             CCccc
Q 003463          311 PGGAR  315 (818)
Q Consensus       311 ~~~~r  315 (818)
                      +....
T Consensus        83 ~~~~~   87 (104)
T d1weya_          83 TLHIG   87 (104)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            76543

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=4.9e-13  Score=119.39  Aligned_cols=81  Identities=10%  Similarity=0.217  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE---eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          148 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       148 ~e~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~---~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ......+|||+|||+++|+++|+++|+.||.+....   ..++.+|||||+|.+.++|++|++ +++..|.||.|+|.++
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345567999999999999999999999998543222   367789999999999999999987 8999999999999998


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        90 ~~~~~   94 (102)
T d1weza_          90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76553

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=2.1e-13  Score=117.81  Aligned_cols=74  Identities=22%  Similarity=0.296  Sum_probs=65.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE---EE--eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          151 PSRTLFVRNINSNVEDSELRALFEQYGDIRT---LY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~---v~--~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..++|||+|||+++++++|+++|+.||.|..   +.  .+++++|+|||+|.+.++|++|++.|++..|.|++|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4567999999999999999999999998743   11  36788999999999999999999999999999999999764

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.35  E-value=7.4e-13  Score=115.43  Aligned_cols=78  Identities=14%  Similarity=0.148  Sum_probs=69.5

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHh--cCcccccccccccccC
Q 003463          149 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~-vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~L--ng~~l~gr~L~V~~a~  225 (818)
                      ..++++|||+|||.. +|++||+++|++||+|..+.+. +.+++|||+|.+.++|+.|++.+  ++..+.|++|+|.|+.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~-~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~   83 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   83 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEee-ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECC
Confidence            467899999999986 8999999999999999999874 46789999999999999999976  5667999999999987


Q ss_pred             CC
Q 003463          226 PK  227 (818)
Q Consensus       226 pk  227 (818)
                      ..
T Consensus        84 ~~   85 (89)
T d1x4da1          84 KY   85 (89)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=5.9e-13  Score=118.82  Aligned_cols=78  Identities=13%  Similarity=0.196  Sum_probs=67.5

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhhccCCeEEEE----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          235 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ....+|||+|||+++|++||+++|+.||.+ .|+    ..+..+|||||+|.+.++|++|++ ||++.|.||.|+|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            345689999999999999999999999854 443    245668999999999999999986 89999999999999998


Q ss_pred             CCcc
Q 003463          311 PGGA  314 (818)
Q Consensus       311 ~~~~  314 (818)
                      +...
T Consensus        91 ~~~~   94 (102)
T d1weza_          91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.35  E-value=5.3e-13  Score=118.64  Aligned_cols=79  Identities=16%  Similarity=0.212  Sum_probs=69.9

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHH--HhcCcccccccccccccC
Q 003463          149 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR--ALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       149 e~~srtLfV~NLP~~-vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~--~Lng~~l~gr~L~V~~a~  225 (818)
                      ..++++|||+|||.+ +|+++|+++|++||.|..+.+ .+.+|+|||+|.+.++|.+|++  .+++..+.|+.|+|.|+.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~-~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~   93 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE   93 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE-eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcC
Confidence            456789999999986 899999999999999999986 3568999999999999999998  467888999999999996


Q ss_pred             CCC
Q 003463          226 PKD  228 (818)
Q Consensus       226 pk~  228 (818)
                      .+.
T Consensus        94 ~~~   96 (99)
T d1x4fa1          94 KYK   96 (99)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            543

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.34  E-value=2.7e-13  Score=118.17  Aligned_cols=72  Identities=18%  Similarity=0.319  Sum_probs=63.6

Q ss_pred             CCcEEEEcCCCCCCcHHHH---HHHhhcCCCEEEEEe-----C---CCcccEEEEEEccHHHHHHHHHHhcCcccccccc
Q 003463          151 PSRTLFVRNINSNVEDSEL---RALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  219 (818)
Q Consensus       151 ~srtLfV~NLP~~vTEeeL---r~lFs~fG~I~~v~~-----~---~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L  219 (818)
                      ..++|||+|||+++++++|   +++|++||+|..|.+     +   ...+|||||+|.+.++|++|++.|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3568999999999999999   678999999999984     1   2245899999999999999999999999999999


Q ss_pred             ccc
Q 003463          220 DIH  222 (818)
Q Consensus       220 ~V~  222 (818)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.30  E-value=7.8e-13  Score=118.70  Aligned_cols=79  Identities=19%  Similarity=0.190  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCcH-----HHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVED-----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTE-----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ..+++|||+||+.++.+     ++|+++|++||.|.+++. .++++||||+|.+.++|++|++.|+|..|.|++|+|.|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~-~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   81 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFA   81 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE-ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEE-ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeec
Confidence            45789999999988633     569999999999999976 468999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003463          225 IPKDN  229 (818)
Q Consensus       225 ~pk~~  229 (818)
                      .++..
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            77654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=1.4e-12  Score=116.31  Aligned_cols=75  Identities=12%  Similarity=0.174  Sum_probs=66.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEE-EE----ecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~-vr----~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||+++|++||+++|+.||.|.. +.    .++.++|+|||+|.+.++|++|++ ||+..|.|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            3468999999999999999999999998864 32    256779999999999999999996 99999999999999875


Q ss_pred             C
Q 003463          311 P  311 (818)
Q Consensus       311 ~  311 (818)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1.2e-12  Score=116.87  Aligned_cols=75  Identities=16%  Similarity=0.202  Sum_probs=66.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE-EE----eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~-v~----~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ....+|||+|||+++|+++|+++|+.||.|.. +.    ..++++|||||+|.+.++|++|++ +++..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            34578999999999999999999999998754 22    367889999999999999999997 8999999999999876


Q ss_pred             C
Q 003463          225 I  225 (818)
Q Consensus       225 ~  225 (818)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=2.9e-13  Score=117.91  Aligned_cols=71  Identities=17%  Similarity=0.332  Sum_probs=63.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE----------eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY----------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  222 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~----------~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~  222 (818)
                      |+|||+|||.++||++|+++|++||.|..+.          .+++++|||||+|.+.++|++|++ |+|..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            7899999999999999999999999765443          245689999999999999999996 99999999999997


Q ss_pred             cc
Q 003463          223 FS  224 (818)
Q Consensus       223 ~a  224 (818)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=3.7e-13  Score=117.25  Aligned_cols=71  Identities=18%  Similarity=0.327  Sum_probs=62.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe----------cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEE
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  307 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----------~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~  307 (818)
                      ++|||+|||.++|+++|+++|+.||.|..+.+          ++.++|||||+|.+.++|++|++ |||..+.|++|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            47999999999999999999999998765532          34678999999999999999985 99999999999997


Q ss_pred             ec
Q 003463          308 PS  309 (818)
Q Consensus       308 ~a  309 (818)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=4.2e-12  Score=115.15  Aligned_cols=76  Identities=9%  Similarity=0.177  Sum_probs=66.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE---E--eCCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          150 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL---Y--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       150 ~~srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v---~--~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      ...++|||+|||+++|+++|+++|+.||.|..+   .  ..++.+|||||+|.+.++|++|++ +++..|.|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            456799999999999999999999999986432   1  468899999999999999999997 8999999999999876


Q ss_pred             CC
Q 003463          225 IP  226 (818)
Q Consensus       225 ~p  226 (818)
                      .+
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
Confidence            43

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=6.3e-12  Score=113.98  Aligned_cols=77  Identities=17%  Similarity=0.203  Sum_probs=66.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEE-----EecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~v-----r~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      ...+|||+|||+++|++||+++|+.||.|..+     ..++.++|+|||+|.+.++|++|++ |||..|+|+.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            34589999999999999999999999987542     2356778999999999999999996 99999999999999876


Q ss_pred             CCc
Q 003463          311 PGG  313 (818)
Q Consensus       311 ~~~  313 (818)
                      +..
T Consensus        96 ~~~   98 (112)
T d1wela1          96 KKG   98 (112)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=2.1e-12  Score=115.82  Aligned_cols=72  Identities=24%  Similarity=0.272  Sum_probs=67.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEe----cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEEEEec
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  309 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~----~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a  309 (818)
                      ..++|.+++.++++++|+++|++||.|++|++    +++++|+|||+|.+.++|.+|++.|||+.+.||+|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46889999999999999999999999999986    4567899999999999999999999999999999999986

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=1.9e-11  Score=108.93  Aligned_cols=66  Identities=18%  Similarity=0.329  Sum_probs=59.8

Q ss_pred             CCCCcEEEEcC--CCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccc
Q 003463          149 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  215 (818)
Q Consensus       149 e~~srtLfV~N--LP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~  215 (818)
                      ..|+++|+|.|  ||.++|+++|+++|++||.|..|++ .+.++||||+|.+.++|++|++.|+|..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~-~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee-ccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            46789999955  9999999999999999999999975 456899999999999999999999998874

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=3.5e-11  Score=107.09  Aligned_cols=64  Identities=23%  Similarity=0.366  Sum_probs=57.5

Q ss_pred             Cccceeeec--CCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccC
Q 003463          236 NQGTLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  300 (818)
Q Consensus       236 ~~~tL~V~N--Lp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~  300 (818)
                      ...+|+|.|  ||..+|+++|+++|++||.|+.|++.. .++||||+|.+.++|.+|++.|||+.+.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~-~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc-CccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            345788865  999999999999999999999998854 5789999999999999999999999873

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=4.7e-11  Score=105.87  Aligned_cols=82  Identities=18%  Similarity=0.293  Sum_probs=70.9

Q ss_pred             CCCCCCcEEEEcCC--CCCCc---------HHHHHHHhhcCCCEEEEEe-CCCcccEEEEEEccHHHHHHHHHHhcCccc
Q 003463          147 YGEHPSRTLFVRNI--NSNVE---------DSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPL  214 (818)
Q Consensus       147 ~~e~~srtLfV~NL--P~~vT---------EeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l  214 (818)
                      .....+++|+|+|+  |.++.         +++|++.|++||.|..|++ ....+|+|||+|.+.++|.+|+..|+|..+
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            34567899999999  65432         3689999999999999884 566789999999999999999999999999


Q ss_pred             ccccccccccCCCC
Q 003463          215 RRRKLDIHFSIPKD  228 (818)
Q Consensus       215 ~gr~L~V~~a~pk~  228 (818)
                      .|++|.|.|..++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987654

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=3.9e-11  Score=108.89  Aligned_cols=76  Identities=21%  Similarity=0.193  Sum_probs=66.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCH-HHHHHHHHHcCCCccCCceEEEEecCCCcc
Q 003463          238 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV-RAAEAALKSLNRSDIAGKRIKLEPSRPGGA  314 (818)
Q Consensus       238 ~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~-e~A~~Ai~~LnG~~i~Gr~L~V~~a~~~~~  314 (818)
                      -.+||+|||+.+|+++|+++|++||+|..|++. ..+++|||+|.+. ++|.+|+..|++..+.++.+.|.++...+.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~   88 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGE   88 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHH
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccch
Confidence            356999999999999999999999999999986 5689999999985 789999999999999887777777665543

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=7.1e-11  Score=104.68  Aligned_cols=78  Identities=17%  Similarity=0.290  Sum_probs=67.4

Q ss_pred             CccceeeecC--CCCC---------CHHHHHHHhhccCCeEEEEe-cCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce
Q 003463          236 NQGTLVVFNL--DPSV---------SNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  303 (818)
Q Consensus       236 ~~~tL~V~NL--p~~v---------teedL~~lFs~fG~I~~vr~-~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~  303 (818)
                      ..++|+|.||  |.++         .++||++.|++||.|..|++ .+..+|+|||+|.+.++|.+|+..|||..+.||+
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~   86 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQ   86 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEE
Confidence            4578999999  5432         13689999999999999976 4566899999999999999999999999999999


Q ss_pred             EEEEecCCCc
Q 003463          304 IKLEPSRPGG  313 (818)
Q Consensus       304 L~V~~a~~~~  313 (818)
                      |+|+|+.++.
T Consensus        87 i~v~~~~g~~   96 (99)
T d2dita1          87 ITAQAWDGTT   96 (99)
T ss_dssp             CEEEECCSCC
T ss_pred             EEEEEeCCcC
Confidence            9999987654

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.08  E-value=7.7e-11  Score=100.70  Aligned_cols=74  Identities=16%  Similarity=0.193  Sum_probs=63.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCce-EEEEecCCC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-IKLEPSRPG  312 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~-L~V~~a~~~  312 (818)
                      ++..|+|.|+|++.+++.| +.|++||+|.++++ +..++||||+|.+.++|++||+ +||..++|+. |.|..+..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            4567999999999886555 57999999999987 4568999999999999999996 9999999975 678887654

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.3e-11  Score=110.46  Aligned_cols=72  Identities=14%  Similarity=0.225  Sum_probs=67.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEEccHHHHHHHHHHhcCccccccccccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  224 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a  224 (818)
                      +.++|++++.+++|++|+++|++||+|.+|++    +++++|||||+|.+.++|++|++.|+|+.+.|++|.|.|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46889999999999999999999999999985    5678999999999999999999999999999999999986

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.4e-10  Score=105.08  Aligned_cols=73  Identities=15%  Similarity=0.243  Sum_probs=64.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccH-HHHHHHHHHhcCcccccccccccccCC
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI-RAARTAMRALQNKPLRRRKLDIHFSIP  226 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~-e~A~~Al~~Lng~~l~gr~L~V~~a~p  226 (818)
                      ..+||+|||.++|+++|+++|++||+|..|.+. +.+|||||.|.+. ++|..|+..+++..+.++.+.|.+...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            456999999999999999999999999999874 5689999999995 789999999999999888888877643

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.93  E-value=5.5e-10  Score=95.25  Aligned_cols=72  Identities=18%  Similarity=0.207  Sum_probs=61.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCccccccc-ccccccCC
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK-LDIHFSIP  226 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~-L~V~~a~p  226 (818)
                      .+.|+|.++|++++++.| +.|++||+|.+++. .+.+|||||+|.+.++|++||+ ++|..|.|+. |.|..+..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            467999999999997655 57999999999975 5678999999999999999996 8999999985 56776653

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=8.9e-10  Score=98.25  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=64.2

Q ss_pred             CccceeeecC--CCCCC--------HHHHHHHhhccCCeEEEEecC-------CCCceEEEEEcCHHHHHHHHHHcCCCc
Q 003463          236 NQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRETP-------HKRHHKFIEFYDVRAAEAALKSLNRSD  298 (818)
Q Consensus       236 ~~~tL~V~NL--p~~vt--------eedL~~lFs~fG~I~~vr~~g-------~srG~aFVeF~d~e~A~~Ai~~LnG~~  298 (818)
                      ..++|.|.|+  +..+.        .+||++.|++||.|++|.+..       ...|++||+|.+.++|.+|++.|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3567999999  44432        367999999999999998632       235899999999999999999999999


Q ss_pred             cCCceEEEEecCC
Q 003463          299 IAGKRIKLEPSRP  311 (818)
Q Consensus       299 i~Gr~L~V~~a~~  311 (818)
                      ++||.|+|.|..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.82  E-value=1.9e-09  Score=96.06  Aligned_cols=77  Identities=17%  Similarity=0.375  Sum_probs=65.8

Q ss_pred             CCCcEEEEcCC--CCCCc--------HHHHHHHhhcCCCEEEEEeC-------CCcccEEEEEEccHHHHHHHHHHhcCc
Q 003463          150 HPSRTLFVRNI--NSNVE--------DSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMRALQNK  212 (818)
Q Consensus       150 ~~srtLfV~NL--P~~vT--------EeeLr~lFs~fG~I~~v~~~-------~ksrG~AFV~F~d~e~A~~Al~~Lng~  212 (818)
                      .|++.|.|+|+  |.++.        .++|++.|++||.|.+|.+.       ....|++||+|.+.++|.+|++.|+|+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            47899999999  55443        35799999999999999852       234689999999999999999999999


Q ss_pred             ccccccccccccCC
Q 003463          213 PLRRRKLDIHFSIP  226 (818)
Q Consensus       213 ~l~gr~L~V~~a~p  226 (818)
                      .+.||.|.+.|..+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999753

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=9.3e-09  Score=88.91  Aligned_cols=84  Identities=21%  Similarity=0.330  Sum_probs=71.6

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcccEE-Eeeecccccce-eEEEEEecCCcccHHHHHHHhcCCcccCCC-CccE
Q 003463          655 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL-YLPIDFKNKCN-VGYAFINMLSPLHIIPFYEAFNGKKWEKFN-SEKV  731 (818)
Q Consensus       655 TtvMirNIPn~~~~~~l~~~id~~~~~~ydf~-Ylp~d~~~~~n-~gyafin~~~~~~~~~f~~~f~g~~w~~~~-s~k~  731 (818)
                      |.|.||++|+.+|++.+++.|+  ..+++||+ |.|-|...+-+ -..|||||.+++++..|.+.|+|+.+..-+ .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~--~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~   79 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQ--PMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHC--SCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhC--CcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEee
Confidence            8999999999999999999998  46889998 47777665543 377999999999999999999999998654 3457


Q ss_pred             EEEEeeecc
Q 003463          732 ASLAYARIQ  740 (818)
Q Consensus       732 ~~~~~A~iQ  740 (818)
                      +.|.||--|
T Consensus        80 a~VE~AP~q   88 (91)
T d1uw4a_          80 AIVEFAPFQ   88 (91)
T ss_dssp             CEEEECSSC
T ss_pred             eEEEEcCcc
Confidence            889998776

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.98  E-value=0.0011  Score=53.25  Aligned_cols=59  Identities=25%  Similarity=0.426  Sum_probs=52.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCc--eEEEEEcCHHHHHHHHHHcCCCccCCceEEEEecC
Q 003463          252 EDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  310 (818)
Q Consensus       252 edL~~lFs~fG~I~~vr~~g~srG--~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~V~~a~  310 (818)
                      +-|...|.++|.|.++.+.+...+  .|-|...+..+|.-|+..|+..+|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345567899999999998766654  69999999999999999999999999999999975

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.43  E-value=0.0023  Score=53.88  Aligned_cols=73  Identities=22%  Similarity=0.399  Sum_probs=57.8

Q ss_pred             CCccceeeecCCCCCC---------HHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcCCCccCCceEE
Q 003463          235 LNQGTLVVFNLDPSVS---------NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  305 (818)
Q Consensus       235 ~~~~tL~V~NLp~~vt---------eedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~LnG~~i~Gr~L~  305 (818)
                      +.+.||.|.=..++..         ..+|.+.|..||+|.-||+..   +...|.|.+-+.|.+|++ ++|.++.|+.|+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~---d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ---GQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET---TEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC---CeEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            3456777754443322         256888999999999999864   568999999999999997 999999999999


Q ss_pred             EEecCC
Q 003463          306 LEPSRP  311 (818)
Q Consensus       306 V~~a~~  311 (818)
                      |..-.+
T Consensus        89 It~~~~   94 (95)
T d1ufwa_          89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            986443

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.54  E-value=0.015  Score=49.30  Aligned_cols=64  Identities=5%  Similarity=0.037  Sum_probs=53.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eCC----C--cccEEEEEEccHHHHHHHHHHhcCccccc
Q 003463          153 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TAC----K--HRGFVMISYYDIRAARTAMRALQNKPLRR  216 (818)
Q Consensus       153 rtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~-~~~----k--srG~AFV~F~d~e~A~~Al~~Lng~~l~g  216 (818)
                      ++|.||.||+.+||+++.+.+...|++.... ..+    +  .-.-|+|.|.+.++.....+.++|..+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            5799999999999999999999999887665 111    1  22369999999999999999999988754

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.28  E-value=0.016  Score=46.46  Aligned_cols=58  Identities=12%  Similarity=0.219  Sum_probs=50.7

Q ss_pred             HHHHHhhcCCCEEEEEeCCCccc--EEEEEEccHHHHHHHHHHhcCcccccccccccccC
Q 003463          168 ELRALFEQYGDIRTLYTACKHRG--FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  225 (818)
Q Consensus       168 eLr~lFs~fG~I~~v~~~~ksrG--~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V~~a~  225 (818)
                      .|.+.|.++|.|.++.+...+.|  .|-|...+..+|..|+..|+...|+.++|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            35578899999999997655554  79999999999999999999999999999998864

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.78  E-value=0.016  Score=48.74  Aligned_cols=70  Identities=19%  Similarity=0.336  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCcH---------HHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhcCcccccccccc
Q 003463          151 PSRTLFVRNINSNVED---------SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  221 (818)
Q Consensus       151 ~srtLfV~NLP~~vTE---------eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Lng~~l~gr~L~V  221 (818)
                      |.-||.|.=...+..+         .+|.+.|..||+|.-++.   -.+-..|+|.+-+.|.+|++ +++..+.|+.|+|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRF---v~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~I   89 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRI---NQGQMLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEE---ETTEEEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEE---eCCeEEEEECCcHHHHHHhc-cCCeEEcceEEEE
Confidence            5678888655444333         368888999999988874   23568999999999999999 8999999999998


Q ss_pred             ccc
Q 003463          222 HFS  224 (818)
Q Consensus       222 ~~a  224 (818)
                      ...
T Consensus        90 t~~   92 (95)
T d1ufwa_          90 SGP   92 (95)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            753

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.46  E-value=0.36  Score=40.80  Aligned_cols=57  Identities=14%  Similarity=0.284  Sum_probs=46.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhhccCCeEEEEecCCCCceEEEEEcCHHHHHHHHHHcC
Q 003463          236 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  295 (818)
Q Consensus       236 ~~~tL~V~NLp~~vteedL~~lFs~fG~I~~vr~~g~srG~aFVeF~d~e~A~~Ai~~Ln  295 (818)
                      .+.-+|.-..|..+...||.++|++||.|.-.-+..   .-|||...+.++|..+++.++
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd---TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD---TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET---TEEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEecC---ceEEEEecCHHHHHHHHHHhc
Confidence            344688888999999999999999999876555543   259999999999999987543

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.76  E-value=1.3  Score=37.28  Aligned_cols=56  Identities=14%  Similarity=0.250  Sum_probs=46.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEEccHHHHHHHHHHhc
Q 003463          152 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  210 (818)
Q Consensus       152 srtLfV~NLP~~vTEeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~d~e~A~~Al~~Ln  210 (818)
                      ...||.-..|..+...||.++|+.||.|.--.+.   .--|||...+.++|+.+++.+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId---dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEec---CceEEEEecCHHHHHHHHHHhc
Confidence            3568888999999999999999999987655442   3369999999999999987554